[{"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"language":[{"iso":"eng"}],"keyword":["Molecular Biology","Structural Biology"],"oa":1,"article_type":"original","publication":"Nature Structural & Molecular Biology","day":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41594-023-01201-6","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01201-6","open_access":"1"}],"pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"year":"2024","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"project":[{"call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445"}],"acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","citation":{"ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. 2024. doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural &#38; Molecular Biology.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology (2024).","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>.","ieee":"J. Datler <i>et al.</i>, “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024.","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., &#38; Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>"},"publisher":"Springer Nature","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"link":[{"url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","description":"News on ISTA Website","relation":"press_release"}]},"ddc":["570"],"status":"public","month":"02","date_updated":"2024-03-05T09:27:47Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses."}],"date_created":"2024-02-12T09:59:45Z","external_id":{"pmid":["38316877"]},"publication_status":"epub_ahead","date_published":"2024-02-05T00:00:00Z","author":[{"orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler"},{"full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","first_name":"Jesse","last_name":"Hansen"},{"last_name":"Thader","first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl"},{"last_name":"Bauer","id":"0c894dcf-897b-11ed-a09c-8186353224b0","first_name":"Lukas W","full_name":"Bauer, Lukas W"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"_id":"14979","quality_controlled":"1","license":"https://creativecommons.org/licenses/by/4.0/"},{"oa":1,"keyword":["Multidisciplinary"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2375-2548"]},"article_number":"add6495","article_type":"original","day":"20","publication":"Science Advances","doi":"10.1126/sciadv.add6495","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nThis research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"year":"2023","article_processing_charge":"No","publisher":"American Association for the Advancement of Science","has_accepted_license":"1","citation":{"ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. <i>Science Advances</i>. 2023;9(3). doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>","ista":"Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V, Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 9(3), add6495.","mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” <i>Science Advances</i>, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>.","short":"F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V. Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).","chicago":"Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner, and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>.","ieee":"F. Fäßler <i>et al.</i>, “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” <i>Science Advances</i>, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","apa":"Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A., … Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>"},"type":"journal_article","file":[{"creator":"dernst","checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","access_level":"open_access","date_created":"2023-01-23T07:45:54Z","file_id":"12335","relation":"main_file","file_name":"2023_ScienceAdvances_Faessler.pdf","content_type":"application/pdf","date_updated":"2023-01-23T07:45:54Z","success":1,"file_size":1756234}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"status":"for_moderation","relation":"research_data","id":"14562"}]},"oa_version":"Published Version","date_updated":"2026-05-21T07:36:27Z","status":"public","month":"01","ddc":["570"],"isi":1,"publication_status":"published","external_id":{"isi":["000964550100015"]},"date_created":"2023-01-23T07:26:42Z","abstract":[{"lang":"eng","text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.</jats:p>"}],"file_date_updated":"2023-01-23T07:45:54Z","scopus_import":"1","volume":9,"author":[{"last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian"},{"last_name":"Javoor","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","full_name":"Javoor, Manjunath"},{"last_name":"Datler","full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hermann","full_name":"Döring, Hermann","last_name":"Döring"},{"id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","first_name":"Florian","full_name":"Hofer, Florian","last_name":"Hofer"},{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"last_name":"Faix","full_name":"Faix, Jan","first_name":"Jan"},{"last_name":"Rottner","full_name":"Rottner, Klemens","first_name":"Klemens"},{"first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"}],"date_published":"2023-01-20T00:00:00Z","intvolume":"         9","quality_controlled":"1","issue":"3","_id":"12334"},{"type":"journal_article","citation":{"ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. <i>Biochemical Society Transactions</i>. 2023;51(1):87-99. doi:<a href=\"https://doi.org/10.1042/bst20220221\">10.1042/bst20220221</a>","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” <i>Biochemical Society Transactions</i>, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:<a href=\"https://doi.org/10.1042/bst20220221\">10.1042/bst20220221</a>.","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99.","chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” <i>Biochemical Society Transactions</i>. Portland Press, 2023. <a href=\"https://doi.org/10.1042/bst20220221\">https://doi.org/10.1042/bst20220221</a>.","apa":"Fäßler, F., Javoor, M., &#38; Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. <i>Biochemical Society Transactions</i>. Portland Press. <a href=\"https://doi.org/10.1042/bst20220221\">https://doi.org/10.1042/bst20220221</a>","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” <i>Biochemical Society Transactions</i>, vol. 51, no. 1. Portland Press, pp. 87–99, 2023."},"has_accepted_license":"1","publisher":"Portland Press","article_processing_charge":"No","isi":1,"ddc":["570"],"status":"public","month":"02","date_updated":"2023-08-01T12:55:32Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","success":1,"file_size":10045006,"content_type":"application/pdf","date_updated":"2023-03-16T07:58:16Z","relation":"main_file","file_id":"12728","checksum":"4e7069845e3dad22bb44fb71ec624c60","creator":"dernst","date_created":"2023-03-16T07:58:16Z","access_level":"open_access"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions."}],"file_date_updated":"2023-03-16T07:58:16Z","publication_status":"published","external_id":{"isi":["000926043100001"]},"date_created":"2023-01-27T10:08:19Z","_id":"12421","quality_controlled":"1","issue":"1","intvolume":"        51","date_published":"2023-02-01T00:00:00Z","author":[{"first_name":"Florian","full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","last_name":"Fäßler"},{"last_name":"Javoor","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","full_name":"Javoor, Manjunath"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur"}],"volume":51,"page":"87-99","article_type":"original","publication_identifier":{"eissn":["1470-8752"],"issn":["0300-5127"]},"language":[{"iso":"eng"}],"oa":1,"keyword":["Biochemistry"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1042/bst20220221","publication":"Biochemical Society Transactions","day":"01","title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","year":"2023","department":[{"_id":"FlSc"}],"project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}],"acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria."},{"ddc":["570"],"isi":1,"status":"public","month":"08","date_updated":"2023-12-13T12:22:22Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_name":"2023_PloSPathogens_Koch.pdf","success":1,"file_size":4458336,"date_updated":"2023-09-06T06:41:52Z","content_type":"application/pdf","relation":"main_file","file_id":"14269","creator":"dernst","checksum":"47ca3bb54b27f28b05644be0ad064bc6","date_created":"2023-09-06T06:41:52Z","access_level":"open_access"}],"type":"journal_article","citation":{"apa":"Koch, J., Xin, Q., Obr, M., Schäfer, A., Rolfs, N., Anagho, H. A., … Lozach, P. Y. (2023). The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>","ieee":"J. Koch <i>et al.</i>, “The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells,” <i>PLoS Pathogens</i>, vol. 19, no. 8. Public Library of Science, 2023.","chicago":"Koch, Jana, Qilin Xin, Martin Obr, Alicia Schäfer, Nina Rolfs, Holda A. Anagho, Aiste Kudulyte, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>.","mla":"Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>.","short":"J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte, L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich, F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023).","ama":"Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. 2023;19(8). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>","ista":"Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FK, Acuna C, Lozach PY. 2023. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 19(8), e1011562."},"has_accepted_license":"1","publisher":"Public Library of Science","article_processing_charge":"Yes","_id":"14255","quality_controlled":"1","issue":"8","intvolume":"        19","date_published":"2023-08-14T00:00:00Z","volume":19,"author":[{"full_name":"Koch, Jana","first_name":"Jana","last_name":"Koch"},{"full_name":"Xin, Qilin","first_name":"Qilin","last_name":"Xin"},{"orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Obr, Martin","last_name":"Obr"},{"full_name":"Schäfer, Alicia","first_name":"Alicia","last_name":"Schäfer"},{"full_name":"Rolfs, Nina","first_name":"Nina","last_name":"Rolfs"},{"last_name":"Anagho","full_name":"Anagho, Holda A.","first_name":"Holda A."},{"full_name":"Kudulyte, Aiste","first_name":"Aiste","last_name":"Kudulyte"},{"last_name":"Woltereck","full_name":"Woltereck, Lea","first_name":"Lea"},{"last_name":"Kummer","full_name":"Kummer, Susann","first_name":"Susann"},{"full_name":"Campos, Joaquin","first_name":"Joaquin","last_name":"Campos"},{"last_name":"Uckeley","full_name":"Uckeley, Zina M.","first_name":"Zina M."},{"last_name":"Bell-Sakyi","full_name":"Bell-Sakyi, Lesley","first_name":"Lesley"},{"full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg","last_name":"Kräusslich"},{"first_name":"Florian Km","full_name":"Schur, Florian Km","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur"},{"full_name":"Acuna, Claudio","first_name":"Claudio","last_name":"Acuna"},{"last_name":"Lozach","first_name":"Pierre Yves","full_name":"Lozach, Pierre Yves"}],"scopus_import":"1","file_date_updated":"2023-09-06T06:41:52Z","abstract":[{"text":"Toscana virus is a major cause of arboviral disease in humans in the Mediterranean basin during summer. However, early virus-host cell interactions and entry mechanisms remain poorly characterized. Investigating iPSC-derived human neurons and cell lines, we found that virus binding to the cell surface was specific, and 50% of bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration required intact late endosomes and occurred within 30 min following internalization. Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of virions to the slightly acidic pH in early endosomes. Strikingly, the particles remained infectious after entering late endosomes with a pH below the fusion threshold. Overall, our study establishes Toscana virus as a late-penetrating virus and reveals an atypical use of vacuolar acidity by this virus to enter host cells.","lang":"eng"}],"date_created":"2023-09-03T22:01:14Z","external_id":{"pmid":["37578957"],"isi":["001050846300004"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1371/journal.ppat.1011562","publication":"PLoS Pathogens","day":"14","article_type":"original","article_number":"e1011562","publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"language":[{"iso":"eng"}],"oa":1,"year":"2023","department":[{"_id":"FlSc"}],"project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"acknowledgement":"We acknowledge Elodie Chatre and the Imaging Platform Platim, SFR Biosciences, Lyon, as well as Vibor Laketa and the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research (CIID) Heidelberg. The sand fly cell lines were supplied by the Tick Cell Biobank at the University of Liverpool. F.K.M.S. acknowledges support from the Scientific Service Units (SSUs) of ISTA through resources provided by the Electron Microscopy Facility (EMF).\r\nThis work was supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (LO-2338/3-1) and the Agence Nationale de la Recherche (ANR) funding (grant numbers ANR-21-CE11-0012 and ANR-22-CE15-0034), all awarded to P.-Y.L. This work was also supported by the LABEX ECOFECT (ANR-11-LABX-0048) of Université de Lyon (UDL), within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the ANR and by the RESPOND program of the UDL (awarded to P.-Y.L) . C.A. was supported by the Chica and Heinz Schaller Research Group funds, NARSAD 2019 award, a Fritz Thyssen Research Grant, and the SFB1158-S02 grant. L.B-S. is supported by a United Kingdom Biotechnology and Biological Sciences Research Council grant (BB/P024270/1) and a Wellcome Trust grant (223743/Z/21/Z). F.K.M.S acknowledges support from the Austrian Science Fund (FWF, P31445). J.K. received a salary from the DFG (LO-2338/3-1) and then from the ANR (ANR-11-LABX-0048). The salary of Z.M.U. was partially covered by the DFG (LO-2338/3-1). S.K. received a salary from the DFG (SFB1129). We are grateful to the Chinese Scholarship Council (CSC; 201904910701), DAAD/ANID (57451854/62180003), the Rufus A. Kellogg fellowship program (Amherst College, Massachusetts, USA) for awarding fellowships to Q.X., J.C., and H.A.A., respectively.","pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells"},{"license":"https://choosealicense.com/licenses/agpl-3.0/","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"department":[{"_id":"FlSc"}],"year":"2023","_id":"14502","author":[{"first_name":"Georgi A","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev"},{"first_name":"Behnam","full_name":"Amiri, Behnam","last_name":"Amiri"},{"last_name":"Fäßler","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Falcke","full_name":"Falcke, Martin","first_name":"Martin"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM"}],"date_published":"2023-11-21T00:00:00Z","date_created":"2023-11-08T19:40:54Z","file_date_updated":"2023-11-21T08:20:23Z","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","abstract":[{"text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.","lang":"eng"}],"doi":"10.15479/AT:ISTA:14502","date_updated":"2023-11-21T08:36:02Z","month":"11","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"day":"21","file":[{"content_type":"application/zip","date_updated":"2023-11-08T20:23:07Z","file_size":347641117,"success":1,"file_name":"Computational_Toolbox_v1.2.zip","relation":"main_file","file_id":"14503","access_level":"open_access","date_created":"2023-11-08T20:23:07Z","creator":"fschur","checksum":"a8b9adeb53a4109dea4d5e39fa1acccf"},{"file_id":"14586","creator":"dernst","checksum":"14db2addbfca61a085ba301ed6f2900b","access_level":"open_access","date_created":"2023-11-21T08:20:23Z","file_name":"Readme.txt","date_updated":"2023-11-21T08:20:23Z","content_type":"text/plain","success":1,"file_size":1522,"relation":"main_file"}],"related_material":{"record":[{"status":"public","id":"10290","relation":"used_for_analysis_in"}]},"tmp":{"short":"GNU AGPLv3  ","legal_code_url":"https://www.gnu.org/licenses/agpl-3.0.html","name":"GNU Affero General Public License v3.0"},"type":"software","oa":1,"keyword":["cryo-electron tomography","actin cytoskeleton","toolbox"],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","citation":{"short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).","mla":"Dimchev, Georgi A., et al. <i>Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>.","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2023). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">https://doi.org/10.15479/AT:ISTA:14502</a>","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data.” Institute of Science and Technology Austria, 2023.","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">https://doi.org/10.15479/AT:ISTA:14502</a>."}},{"month":"03","status":"public","isi":1,"oa_version":"Published Version","date_updated":"2023-08-02T13:52:33Z","type":"journal_article","publisher":"American Society for Microbiology","citation":{"ieee":"S. Windhaber <i>et al.</i>, “The Orthobunyavirus Germiston enters host cells from late endosomes,” <i>Journal of Virology</i>, vol. 96, no. 5. American Society for Microbiology, 2022.","apa":"Windhaber, S., Xin, Q., Uckeley, Z. M., Koch, J., Obr, M., Garnier, C., … Lozach, P.-Y. (2022). The Orthobunyavirus Germiston enters host cells from late endosomes. <i>Journal of Virology</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/jvi.02146-21\">https://doi.org/10.1128/jvi.02146-21</a>","chicago":"Windhaber, Stefan, Qilin Xin, Zina M. Uckeley, Jana Koch, Martin Obr, Céline Garnier, Catherine Luengo-Guyonnot, Maëva Duboeuf, Florian KM Schur, and Pierre-Yves Lozach. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.” <i>Journal of Virology</i>. American Society for Microbiology, 2022. <a href=\"https://doi.org/10.1128/jvi.02146-21\">https://doi.org/10.1128/jvi.02146-21</a>.","short":"S. Windhaber, Q. Xin, Z.M. Uckeley, J. Koch, M. Obr, C. Garnier, C. Luengo-Guyonnot, M. Duboeuf, F.K. Schur, P.-Y. Lozach, Journal of Virology 96 (2022).","mla":"Windhaber, Stefan, et al. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.” <i>Journal of Virology</i>, vol. 96, no. 5, e02146-21, American Society for Microbiology, 2022, doi:<a href=\"https://doi.org/10.1128/jvi.02146-21\">10.1128/jvi.02146-21</a>.","ista":"Windhaber S, Xin Q, Uckeley ZM, Koch J, Obr M, Garnier C, Luengo-Guyonnot C, Duboeuf M, Schur FK, Lozach P-Y. 2022. The Orthobunyavirus Germiston enters host cells from late endosomes. Journal of Virology. 96(5), e02146-21.","ama":"Windhaber S, Xin Q, Uckeley ZM, et al. The Orthobunyavirus Germiston enters host cells from late endosomes. <i>Journal of Virology</i>. 2022;96(5). doi:<a href=\"https://doi.org/10.1128/jvi.02146-21\">10.1128/jvi.02146-21</a>"},"article_processing_charge":"No","_id":"10639","quality_controlled":"1","issue":"5","volume":96,"author":[{"last_name":"Windhaber","first_name":"Stefan","full_name":"Windhaber, Stefan"},{"first_name":"Qilin","full_name":"Xin, Qilin","last_name":"Xin"},{"last_name":"Uckeley","full_name":"Uckeley, Zina M.","first_name":"Zina M."},{"last_name":"Koch","full_name":"Koch, Jana","first_name":"Jana"},{"first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","last_name":"Obr"},{"last_name":"Garnier","first_name":"Céline","full_name":"Garnier, Céline"},{"first_name":"Catherine","full_name":"Luengo-Guyonnot, Catherine","last_name":"Luengo-Guyonnot"},{"last_name":"Duboeuf","full_name":"Duboeuf, Maëva","first_name":"Maëva"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur"},{"first_name":"Pierre-Yves","full_name":"Lozach, Pierre-Yves","last_name":"Lozach"}],"intvolume":"        96","date_published":"2022-03-01T00:00:00Z","scopus_import":"1","abstract":[{"text":"With more than 80 members worldwide, the Orthobunyavirus genus in the Peribunyaviridae family is a large genus of enveloped RNA viruses, many of which are emerging pathogens in humans and livestock. How orthobunyaviruses (OBVs) penetrate and infect mammalian host cells remains poorly characterized. Here, we investigated the entry mechanisms of the OBV Germiston (GERV). Viral particles were visualized by cryo-electron microscopy and appeared roughly spherical with an average diameter of 98 nm. Labeling of the virus with fluorescent dyes did not adversely affect its infectivity and allowed the monitoring of single particles in fixed and live cells. Using this approach, we found that endocytic internalization of bound viruses was asynchronous and occurred within 30-40 min. The virus entered Rab5a+ early endosomes and, subsequently, late endosomal vacuoles containing Rab7a but not LAMP-1. Infectious entry did not require proteolytic cleavage, and endosomal acidification was sufficient and necessary for viral fusion. Acid-activated penetration began 15-25 min after initiation of virus internalization and relied on maturation of early endosomes to late endosomes. The optimal pH for viral membrane fusion was slightly below 6.0, and penetration was hampered when the potassium influx was abolished. Overall, our study provides real-time visualization of GERV entry into host cells and demonstrates the importance of late endosomal maturation in facilitating OBV penetration.","lang":"eng"}],"publication_status":"published","date_created":"2022-01-18T10:04:18Z","external_id":{"pmid":["35019710"],"isi":["000779305000033"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1128/jvi.02146-21","day":"01","publication":"Journal of Virology","article_type":"original","article_number":"e02146-21","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-538X"],"eissn":["1098-5514"]},"oa":1,"keyword":["virology","insect science","immunology","microbiology"],"department":[{"_id":"FlSc"}],"year":"2022","acknowledgement":"This work  was  supported  by  INRAE  starter  funds, Project IDEXLYON  (University  of  Lyon) within  the  Programme  Investissements  d’Avenir  (ANR-16-IDEX-0005),  and  FINOVIAO14 (Fondation  pour  l’Université  de  Lyon),  all  to  P.Y.L.  This  work  was  also  supported  by CellNetworks  Research  Group  funds  and  Deutsche  Forschungsgemeinschaft  (DFG)  funding (grant  numbers  LO-2338/1-1  and  LO-2338/3-1)  awarded  to  P.Y.L., Austrian  Science  Fund (FWF)  grant  P31445  to  F.K.M.S., a  Chinese  Scholarship  Council (CSC;no.  201904910701) fellowship  to   Q.X.,  and  a  ministére  de  l’enseignement  supérieur,  de  la  recherche  et  de l’innovation (MESRI) doctoral thesis grant to M.D.","project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8906410"}],"title":"The Orthobunyavirus Germiston enters host cells from late endosomes"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.jsb.2022.107852","publication":"Journal of Structural Biology","day":"01","article_type":"original","article_number":"107852","publication_identifier":{"issn":["1047-8477"]},"language":[{"iso":"eng"}],"keyword":["Structural Biology"],"oa":1,"year":"2022","department":[{"_id":"FlSc"}],"project":[{"call_identifier":"FWF","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback.","pmid":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs","isi":1,"ddc":["570"],"status":"public","month":"06","date_updated":"2023-08-03T06:25:23Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_id":"11722","creator":"dernst","checksum":"0b1eb53447aae8e95ae4c12d193b0b00","date_created":"2022-08-02T11:07:58Z","access_level":"open_access","file_name":"2022_JourStructuralBiology_Obr.pdf","success":1,"file_size":7080863,"date_updated":"2022-08-02T11:07:58Z","content_type":"application/pdf","relation":"main_file"}],"type":"journal_article","citation":{"chicago":"Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>.","apa":"Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., &#38; Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>","ieee":"M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” <i>Journal of Structural Biology</i>, vol. 214, no. 2. Elsevier, 2022.","ama":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. 2022;214(2). doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>","ista":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852.","short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022).","mla":"Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>, vol. 214, no. 2, 107852, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>."},"has_accepted_license":"1","publisher":"Elsevier","article_processing_charge":"Yes (via OA deal)","_id":"11155","issue":"2","quality_controlled":"1","date_published":"2022-06-01T00:00:00Z","intvolume":"       214","volume":214,"author":[{"last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Obr, Martin"},{"last_name":"Hagen","full_name":"Hagen, Wim J.H.","first_name":"Wim J.H."},{"last_name":"Dick","full_name":"Dick, Robert A.","first_name":"Robert A."},{"last_name":"Yu","full_name":"Yu, Lingbo","first_name":"Lingbo"},{"last_name":"Kotecha","full_name":"Kotecha, Abhay","first_name":"Abhay"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"}],"scopus_import":"1","file_date_updated":"2022-08-02T11:07:58Z","abstract":[{"text":"The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes.","lang":"eng"}],"date_created":"2022-04-15T07:10:26Z","publication_status":"published","external_id":{"isi":["000790733600001"],"pmid":["35351542"]}},{"title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","year":"2022","department":[{"_id":"FlSc"}],"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"acknowledgement":"This work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank Noé Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.","pmid":1,"article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0960-9822"]},"oa":1,"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.cub.2022.04.024","publication":"Current Biology","day":"06","scopus_import":"1","file_date_updated":"2022-08-05T06:29:18Z","abstract":[{"text":"One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000822399200019"],"pmid":["35508170"]},"date_created":"2022-05-04T06:22:06Z","_id":"11351","quality_controlled":"1","issue":"11","intvolume":"        32","date_published":"2022-06-06T00:00:00Z","volume":32,"page":"P2375-2389","author":[{"last_name":"Nicolas","full_name":"Nicolas, William J.","first_name":"William J."},{"last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X"},{"last_name":"Dutka","first_name":"Przemysław","full_name":"Dutka, Przemysław"},{"last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"},{"last_name":"Jensen","full_name":"Jensen, Grant","first_name":"Grant"},{"last_name":"Meyerowitz","full_name":"Meyerowitz, Elliot","first_name":"Elliot"}],"type":"journal_article","citation":{"ieee":"W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz, “Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks,” <i>Current Biology</i>, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022.","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., &#38; Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>","chicago":"Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur, Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>.","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>.","ama":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. 2022;32(11):P2375-2389. doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>","ista":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389."},"has_accepted_license":"1","publisher":"Elsevier","article_processing_charge":"No","ddc":["570"],"isi":1,"month":"06","status":"public","date_updated":"2023-08-03T07:05:36Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_name":"2022_CurrentBiology_Nicolas.pdf","date_updated":"2022-08-05T06:29:18Z","content_type":"application/pdf","file_size":12827717,"success":1,"relation":"main_file","file_id":"11730","creator":"dernst","checksum":"af3f24d97c016d844df237abef987639","access_level":"open_access","date_created":"2022-08-05T06:29:18Z"}]},{"title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly","acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","project":[{"name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","call_identifier":"FWF"}],"department":[{"_id":"FlSc"}],"year":"2021","pmid":1,"article_number":"1853","article_type":"original","keyword":["virology","infectious diseases"],"oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1999-4915"]},"doi":"10.3390/v13091853","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"17","publication":"Viruses","external_id":{"isi":["000699841100001"],"pmid":["34578434"]},"publication_status":"published","date_created":"2021-10-07T09:13:29Z","file_date_updated":"2021-10-08T10:38:15Z","abstract":[{"lang":"eng","text":"The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses."}],"quality_controlled":"1","issue":"9","_id":"10103","author":[{"orcid":"0000-0003-1756-6564","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","last_name":"Obr"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur"},{"first_name":"Robert A.","full_name":"Dick, Robert A.","last_name":"Dick"}],"volume":13,"date_published":"2021-09-17T00:00:00Z","intvolume":"        13","type":"journal_article","article_processing_charge":"Yes","publisher":"MDPI","has_accepted_license":"1","citation":{"ieee":"M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role of IP6 in immature and mature retroviral assembly,” <i>Viruses</i>, vol. 13, no. 9. MDPI, 2021.","apa":"Obr, M., Schur, F. K., &#38; Dick, R. A. (2021). A structural perspective of the role of IP6 in immature and mature retroviral assembly. <i>Viruses</i>. MDPI. <a href=\"https://doi.org/10.3390/v13091853\">https://doi.org/10.3390/v13091853</a>","chicago":"Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” <i>Viruses</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/v13091853\">https://doi.org/10.3390/v13091853</a>.","short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).","mla":"Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” <i>Viruses</i>, vol. 13, no. 9, 1853, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/v13091853\">10.3390/v13091853</a>.","ista":"Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 13(9), 1853.","ama":"Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature and mature retroviral assembly. <i>Viruses</i>. 2021;13(9). doi:<a href=\"https://doi.org/10.3390/v13091853\">10.3390/v13091853</a>"},"oa_version":"Published Version","date_updated":"2023-08-14T07:21:51Z","month":"09","status":"public","isi":1,"ddc":["616"],"file":[{"file_name":"2021_Viruses_Obr.pdf","date_updated":"2021-10-08T10:38:15Z","content_type":"application/pdf","file_size":4146796,"success":1,"relation":"main_file","file_id":"10115","creator":"cchlebak","checksum":"bcfd72a12977d48e22df3d0cc55aacf1","access_level":"open_access","date_created":"2021-10-08T10:38:15Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"publication":"Journal of Structural Biology","day":"03","doi":"10.1016/j.jsb.2021.107808","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"keyword":["Structural Biology"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1047-8477"]},"article_number":"107808","article_type":"original","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales","grant_number":"M02495","call_identifier":"FWF"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.","year":"2021","department":[{"_id":"FlSc"}],"title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"status":"public","id":"14502","relation":"software"}]},"file":[{"relation":"main_file","date_updated":"2021-11-15T13:11:27Z","content_type":"application/pdf","success":1,"file_size":16818304,"file_name":"2021_JournalStructBiol_Dimchev.pdf","access_level":"open_access","date_created":"2021-11-15T13:11:27Z","checksum":"6b209e4d44775d4e02b50f78982c15fa","creator":"cchlebak","file_id":"10291"}],"date_updated":"2023-11-21T08:36:02Z","oa_version":"Published Version","isi":1,"ddc":["572"],"status":"public","month":"11","article_processing_charge":"Yes (via OA deal)","citation":{"ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808.","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. 2021;213(4). doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>","mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>, vol. 213, no. 4, 107808, Elsevier , 2021, doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>. Elsevier , 2021. <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” <i>Journal of Structural Biology</i>, vol. 213, no. 4. Elsevier , 2021."},"has_accepted_license":"1","publisher":"Elsevier ","type":"journal_article","intvolume":"       213","date_published":"2021-11-03T00:00:00Z","volume":213,"author":[{"last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","first_name":"Georgi A"},{"full_name":"Amiri, Behnam","first_name":"Behnam","last_name":"Amiri"},{"full_name":"Fäßler, Florian","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","last_name":"Fäßler"},{"last_name":"Falcke","full_name":"Falcke, Martin","first_name":"Martin"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","issue":"4","_id":"10290","external_id":{"isi":["000720259500002"]},"date_created":"2021-11-15T12:21:42Z","publication_status":"published","file_date_updated":"2021-11-15T13:11:27Z","abstract":[{"text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.","lang":"eng"}],"scopus_import":"1"},{"file_date_updated":"2021-05-28T12:39:43Z","abstract":[{"lang":"eng","text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs."}],"date_created":"2021-05-28T11:49:46Z","publication_status":"published","external_id":{"isi":["000658769900010"]},"intvolume":"        12","date_published":"2021-05-24T00:00:00Z","author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Morandell"},{"first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Lena A","last_name":"Schwarz"},{"last_name":"Basilico","full_name":"Basilico, Bernadette","first_name":"Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173"},{"last_name":"Tasciyan","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","first_name":"Saren"},{"orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev"},{"first_name":"Armel","full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas"},{"last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger"},{"last_name":"Dotter","first_name":"Christoph","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096"},{"first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","last_name":"Knaus"},{"last_name":"Dobler","first_name":"Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","full_name":"Dobler, Zoe"},{"last_name":"Cacci","first_name":"Emanuele","full_name":"Cacci, Emanuele"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur"},{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino"}],"volume":12,"_id":"9429","quality_controlled":"1","issue":"1","citation":{"mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021).","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>","ieee":"J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>."},"publisher":"Springer Nature","has_accepted_license":"1","article_processing_charge":"No","type":"journal_article","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"7800"},{"relation":"dissertation_contains","id":"12401","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_id":"9430","access_level":"open_access","date_created":"2021-05-28T12:39:43Z","checksum":"337e0f7959c35ec959984cacdcb472ba","creator":"kschuh","date_updated":"2021-05-28T12:39:43Z","content_type":"application/pdf","file_size":9358599,"success":1,"file_name":"2021_NatureCommunications_Morandell.pdf","relation":"main_file"}],"isi":1,"ddc":["572"],"month":"05","status":"public","date_updated":"2024-09-10T12:04:26Z","oa_version":"Published Version","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","acknowledged_ssus":[{"_id":"PreCl"}],"year":"2021","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","name":"Neural stem cells in autism and epilepsy","grant_number":"F07807"},{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600"}],"acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"oa":1,"ec_funded":1,"article_type":"original","article_number":"3058","publication":"Nature Communications","day":"24","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-021-23123-x"},{"oa_version":"Published Version","date_updated":"2023-08-08T13:53:53Z","status":"public","month":"05","ddc":["570"],"isi":1,"file":[{"relation":"main_file","file_name":"2021_NatureCommunications_Obr.pdf","date_updated":"2021-06-09T15:21:14Z","content_type":"application/pdf","success":1,"file_size":6166295,"creator":"kschuh","checksum":"53ccc53d09a9111143839dbe7784e663","access_level":"open_access","date_created":"2021-06-09T15:21:14Z","file_id":"9538"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/","description":"News on IST Homepage"}]},"type":"journal_article","article_processing_charge":"No","has_accepted_license":"1","publisher":"Nature Research","citation":{"apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>","ieee":"M. Obr <i>et al.</i>, “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” <i>Nature Communications</i>, vol. 12, no. 1. Nature Research, 2021.","chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>.","mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>, vol. 12, no. 1, 3226, Nature Research, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>.","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226."},"quality_controlled":"1","issue":"1","_id":"9431","volume":12,"author":[{"first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","last_name":"Obr"},{"last_name":"Ricana","first_name":"Clifton L.","full_name":"Ricana, Clifton L."},{"last_name":"Nikulin","first_name":"Nadia","full_name":"Nikulin, Nadia"},{"first_name":"Jon-Philip R.","full_name":"Feathers, Jon-Philip R.","last_name":"Feathers"},{"last_name":"Klanschnig","full_name":"Klanschnig, Marco","first_name":"Marco"},{"id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas","first_name":"Andreas","last_name":"Thader"},{"last_name":"Johnson","full_name":"Johnson, Marc C.","first_name":"Marc C."},{"last_name":"Vogt","first_name":"Volker M.","full_name":"Vogt, Volker M."},{"last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dick","full_name":"Dick, Robert A.","first_name":"Robert A."}],"intvolume":"        12","date_published":"2021-05-28T00:00:00Z","scopus_import":"1","publication_status":"published","external_id":{"isi":["000659145000011"]},"date_created":"2021-05-28T14:25:50Z","abstract":[{"text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.","lang":"eng"}],"file_date_updated":"2021-06-09T15:21:14Z","doi":"10.1038/s41467-021-23506-0","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"28","publication":"Nature Communications","article_number":"3226","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF).","project":[{"call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445"}],"department":[{"_id":"FlSc"}],"year":"2021","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer"},{"status":"public","month":"12","isi":1,"ddc":["570"],"oa_version":"Published Version","date_updated":"2024-03-25T23:30:04Z","file":[{"access_level":"open_access","date_created":"2020-12-10T14:01:10Z","creator":"dernst","checksum":"c48cbf594e84fc2f91966ffaafc0918c","file_id":"8937","relation":"main_file","content_type":"application/pdf","date_updated":"2020-12-10T14:01:10Z","file_size":7076870,"success":1,"file_name":"2020_JourStrucBiology_Faessler.pdf"}],"related_material":{"record":[{"relation":"used_in_publication","id":"14592","status":"public"},{"status":"public","id":"12491","relation":"dissertation_contains"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","publisher":"Elsevier","has_accepted_license":"1","citation":{"chicago":"Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>.","apa":"Fäßler, F., Zens, B., Hauschild, R., &#38; Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>","ieee":"F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” <i>Journal of Structural Biology</i>, vol. 212, no. 3. Elsevier, 2020.","ista":"Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633.","ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. 2020;212(3). doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>","mla":"Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>, vol. 212, no. 3, 107633, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>.","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020)."},"article_processing_charge":"Yes (via OA deal)","_id":"8586","issue":"3","quality_controlled":"1","author":[{"first_name":"Florian","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler"},{"last_name":"Zens","first_name":"Bettina","full_name":"Zens, Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"volume":212,"date_published":"2020-12-01T00:00:00Z","intvolume":"       212","scopus_import":"1","file_date_updated":"2020-12-10T14:01:10Z","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"date_created":"2020-09-29T13:24:06Z","publication_status":"published","external_id":{"isi":["000600997800008"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.jsb.2020.107633","day":"01","publication":"Journal of Structural Biology","article_type":"original","article_number":"107633","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1047-8477"]},"keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"oa":1,"department":[{"_id":"FlSc"}],"year":"2020","acknowledgement":"This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract.","project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy"},{"title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"year":"2020","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"call_identifier":"FWF","grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-1723"]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"oa":1,"article_type":"original","article_number":"6437","publication":"Nature Communications","day":"22","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-020-20286-x","abstract":[{"text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.","lang":"eng"}],"file_date_updated":"2020-12-28T08:16:10Z","external_id":{"isi":["000603078000003"]},"publication_status":"published","date_created":"2020-12-23T08:25:45Z","scopus_import":"1","date_published":"2020-12-22T00:00:00Z","intvolume":"        11","author":[{"orcid":"0000-0001-7149-769X","first_name":"Florian","full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler"},{"first_name":"Georgi A","full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","last_name":"Dimchev"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"full_name":"Wan, William","first_name":"William","last_name":"Wan"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur"}],"volume":11,"_id":"8971","quality_controlled":"1","citation":{"chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>.","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., &#38; Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>, vol. 11, 6437, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020)."},"has_accepted_license":"1","publisher":"Springer Nature","article_processing_charge":"No","type":"journal_article","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","relation":"press_release"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"relation":"main_file","file_size":3958727,"success":1,"content_type":"application/pdf","date_updated":"2020-12-28T08:16:10Z","file_name":"2020_NatureComm_Faessler.pdf","date_created":"2020-12-28T08:16:10Z","access_level":"open_access","creator":"dernst","checksum":"55d43ea0061cc4027ba45e966e1db8cc","file_id":"8975"}],"ddc":["570"],"isi":1,"status":"public","month":"12","date_updated":"2023-08-24T11:01:50Z","oa_version":"Published Version"},{"_id":"7464","issue":"1","quality_controlled":"1","date_published":"2020-01-27T00:00:00Z","intvolume":"        16","author":[{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"},{"last_name":"Xu","full_name":"Xu, Chaoyi","first_name":"Chaoyi"},{"last_name":"Morado","full_name":"Morado, Dustin R.","first_name":"Dustin R."},{"first_name":"Vladyslav","full_name":"Kravchuk, Vladyslav","orcid":"0000-0001-9523-9089","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","last_name":"Kravchuk"},{"last_name":"Ricana","first_name":"Clifton L.","full_name":"Ricana, Clifton L."},{"last_name":"Lyddon","full_name":"Lyddon, Terri D.","first_name":"Terri D."},{"full_name":"Broad, Arianna M.","first_name":"Arianna M.","last_name":"Broad"},{"last_name":"Feathers","full_name":"Feathers, J. Ryan","first_name":"J. Ryan"},{"last_name":"Johnson","full_name":"Johnson, Marc C.","first_name":"Marc C."},{"full_name":"Vogt, Volker M.","first_name":"Volker M.","last_name":"Vogt"},{"last_name":"Perilla","full_name":"Perilla, Juan R.","first_name":"Juan R."},{"last_name":"Briggs","first_name":"John A. G.","full_name":"Briggs, John A. G."},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"volume":16,"scopus_import":"1","abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:59Z","publication_status":"published","external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"date_created":"2020-02-06T18:47:17Z","ddc":["570"],"isi":1,"month":"01","status":"public","date_updated":"2023-10-17T12:29:34Z","oa_version":"Published Version","related_material":{"record":[{"relation":"research_data","id":"9723","status":"deleted"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_id":"7484","creator":"dernst","checksum":"a297f54d1fef0efe4789ca00f37f241e","access_level":"open_access","date_created":"2020-02-11T10:07:28Z","file_name":"2020_PLOSPatho_Dick.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:59Z","file_size":4551246,"relation":"main_file"}],"type":"journal_article","citation":{"chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>.","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>","ieee":"R. A. Dick <i>et al.</i>, “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” <i>PLOS Pathogens</i>, vol. 16, no. 1. Public Library of Science, 2020.","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. 2020;16(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>.","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020)."},"has_accepted_license":"1","publisher":"Public Library of Science","article_processing_charge":"No","year":"2020","department":[{"_id":"FlSc"}],"project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1371/journal.ppat.1008277","publication":"PLOS Pathogens","day":"27","article_type":"original","article_number":"e1008277","publication_identifier":{"issn":["1553-7374"]},"language":[{"iso":"eng"}],"oa":1},{"type":"research_data","article_processing_charge":"No","oa":1,"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","citation":{"ama":"Schur FK. STL-files for 3D-printed grid holders described in  Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14592\">10.15479/AT:ISTA:14592</a>","ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in  Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14592\">10.15479/AT:ISTA:14592</a>.","mla":"Schur, Florian KM. <i>STL-Files for 3D-Printed Grid Holders Described in  Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14592\">10.15479/AT:ISTA:14592</a>.","short":"F.K. Schur, (2020).","chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in  Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:14592\">https://doi.org/10.15479/AT:ISTA:14592</a>.","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in  Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14592\">https://doi.org/10.15479/AT:ISTA:14592</a>","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in  Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020."},"oa_version":"Published Version","doi":"10.15479/AT:ISTA:14592","date_updated":"2024-02-21T12:44:48Z","month":"12","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","file":[{"relation":"main_file","file_name":"3Dprint-files_download_v2.zip","content_type":"application/zip","date_updated":"2023-11-22T14:58:44Z","success":1,"file_size":49297,"checksum":"0108616e2a59e51879ea51299a29b091","creator":"fschur","access_level":"open_access","date_created":"2023-11-22T14:58:44Z","file_id":"14593"},{"relation":"main_file","file_name":"readme.txt","content_type":"text/plain","date_updated":"2023-12-01T10:39:59Z","file_size":641,"success":1,"checksum":"4c66ddedee4d01c1c4a7978208350cfc","creator":"cchlebak","access_level":"open_access","date_created":"2023-12-01T10:39:59Z","file_id":"14637"}],"related_material":{"record":[{"status":"public","id":"8586","relation":"research_data"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"contributor":[{"last_name":"Fäßler","contributor_type":"researcher","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X"},{"first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","contributor_type":"researcher"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","contributor_type":"researcher"},{"orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Schur"}],"date_created":"2023-11-22T15:00:57Z","file_date_updated":"2023-12-01T10:39:59Z","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"title":"STL-files for 3D-printed grid holders described in  Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"department":[{"_id":"FlSc"}],"_id":"14592","year":"2020","author":[{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur"}],"date_published":"2020-12-01T00:00:00Z"},{"_id":"6343","issue":"10","quality_controlled":"1","author":[{"last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"}],"page":"1-9","volume":58,"intvolume":"        58","date_published":"2019-10-01T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein’s location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA."}],"publication_status":"published","external_id":{"isi":["000494891800004"]},"date_created":"2019-04-19T11:19:13Z","status":"public","month":"10","isi":1,"oa_version":"None","date_updated":"2023-08-25T10:13:31Z","type":"journal_article","publisher":"Elsevier","citation":{"ista":"Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10), 1–9.","ama":"Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. <i>Current Opinion in Structural Biology</i>. 2019;58(10):1-9. doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">10.1016/j.sbi.2019.03.018</a>","short":"F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9.","mla":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” <i>Current Opinion in Structural Biology</i>, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">10.1016/j.sbi.2019.03.018</a>.","chicago":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">https://doi.org/10.1016/j.sbi.2019.03.018</a>.","ieee":"F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging,” <i>Current Opinion in Structural Biology</i>, vol. 58, no. 10. Elsevier, pp. 1–9, 2019.","apa":"Schur, F. K. (2019). Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">https://doi.org/10.1016/j.sbi.2019.03.018</a>"},"article_processing_charge":"No","department":[{"_id":"FlSc"}],"year":"2019","acknowledgement":"The author acknowledges support from IST Austria and the Austrian Science Fund (FWF).","title":"Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.sbi.2019.03.018","day":"01","publication":"Current Opinion in Structural Biology","article_type":"original","publication_identifier":{"issn":["0959-440X"]},"language":[{"iso":"eng"}]},{"_id":"6890","quality_controlled":"1","author":[{"last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","first_name":"Martin","full_name":"Obr, Martin"},{"last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"page":"117-159","volume":105,"intvolume":"       105","date_published":"2019-08-27T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods."}],"external_id":{"isi":["000501594500006"],"pmid":["    31522703"]},"publication_status":"published","date_created":"2019-09-18T08:15:37Z","month":"08","status":"public","isi":1,"oa_version":"None","date_updated":"2023-08-30T06:56:00Z","series_title":"Advances in Virus Research","type":"book_chapter","publisher":"Elsevier","citation":{"ama":"Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. <i>Complementary Strategies to Study Virus Structure and Function</i>. Vol 105. Advances in Virus Research. Elsevier; 2019:117-159. doi:<a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">10.1016/bs.aivir.2019.07.008</a>","ista":"Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies to Study Virus Structure and Function. vol. 105, 117–159.","mla":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” <i>Complementary Strategies to Study Virus Structure and Function</i>, edited by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:<a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">10.1016/bs.aivir.2019.07.008</a>.","short":"M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function, Elsevier, 2019, pp. 117–159.","chicago":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” In <i>Complementary Strategies to Study Virus Structure and Function</i>, edited by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. <a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">https://doi.org/10.1016/bs.aivir.2019.07.008</a>.","apa":"Obr, M., &#38; Schur, F. K. (2019). Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In F. A. Rey (Ed.), <i>Complementary Strategies to Study Virus Structure and Function</i> (Vol. 105, pp. 117–159). Elsevier. <a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">https://doi.org/10.1016/bs.aivir.2019.07.008</a>","ieee":"M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging,” in <i>Complementary Strategies to Study Virus Structure and Function</i>, vol. 105, F. A. Rey, Ed. Elsevier, 2019, pp. 117–159."},"article_processing_charge":"No","department":[{"_id":"FlSc"}],"year":"2019","pmid":1,"title":"Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","editor":[{"last_name":"Rey","first_name":"Félix A.","full_name":"Rey, Félix A."}],"doi":"10.1016/bs.aivir.2019.07.008","day":"27","publication":"Complementary Strategies to Study Virus Structure and Function","publication_identifier":{"issn":["0065-3527"],"isbn":["9780128184561"]},"language":[{"iso":"eng"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1038/s41586-018-0396-4","day":"29","publication":"Nature","article_type":"original","publication_identifier":{"eissn":["1476-4687"]},"language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"FlSc"}],"year":"2018","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"title":"Inositol phosphates are assembly co-factors for HIV-1","month":"08","status":"public","isi":1,"oa_version":"Submitted Version","date_updated":"2023-09-12T07:44:37Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-018-0505-4"}]},"type":"journal_article","publisher":"Nature Publishing Group","citation":{"ieee":"R. Dick <i>et al.</i>, “Inositol phosphates are assembly co-factors for HIV-1,” <i>Nature</i>, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>.","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512.","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>.","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. 2018;560(7719):509–512. doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512."},"article_processing_charge":"No","_id":"150","quality_controlled":"1","issue":"7719","author":[{"last_name":"Dick","full_name":"Dick, Robert","first_name":"Robert"},{"full_name":"Zadrozny, Kaneil K","first_name":"Kaneil K","last_name":"Zadrozny"},{"first_name":"Chaoyi","full_name":"Xu, Chaoyi","last_name":"Xu"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Terri D","full_name":"Lyddon, Terri D","last_name":"Lyddon"},{"full_name":"Ricana, Clifton L","first_name":"Clifton L","last_name":"Ricana"},{"last_name":"Wagner","first_name":"Jonathan M","full_name":"Wagner, Jonathan M"},{"last_name":"Perilla","first_name":"Juan R","full_name":"Perilla, Juan R"},{"last_name":"Ganser","full_name":"Ganser, Pornillos Barbie K","first_name":"Pornillos Barbie K"},{"last_name":"Johnson","full_name":"Johnson, Marc C","first_name":"Marc C"},{"last_name":"Pornillos","first_name":"Owen","full_name":"Pornillos, Owen"},{"last_name":"Vogt","full_name":"Vogt, Volker","first_name":"Volker"}],"page":"509–512","volume":560,"date_published":"2018-08-29T00:00:00Z","intvolume":"       560","scopus_import":"1","abstract":[{"text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.","lang":"eng"}],"publication_status":"published","external_id":{"pmid":["30158708"],"isi":["000442483400046"]},"date_created":"2018-12-11T11:44:53Z"},{"month":"12","status":"public","isi":1,"oa_version":"Submitted Version","date_updated":"2023-09-19T09:57:45Z","publisher":"Proceedings of the National Academy of Sciences","citation":{"apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1811580115\">https://doi.org/10.1073/pnas.1811580115</a>","ieee":"K. Qu <i>et al.</i>, “Structure and architecture of immature and mature murine leukemia virus capsids,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760, 2018.","chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1811580115\">https://doi.org/10.1073/pnas.1811580115</a>.","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:<a href=\"https://doi.org/10.1073/pnas.1811580115\">10.1073/pnas.1811580115</a>.","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences 115 (2018) E11751–E11760.","ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(50):E11751-E11760. doi:<a href=\"https://doi.org/10.1073/pnas.1811580115\">10.1073/pnas.1811580115</a>","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 115(50), E11751–E11760."},"article_processing_charge":"No","type":"journal_article","page":"E11751-E11760","author":[{"full_name":"Qu, Kun","first_name":"Kun","last_name":"Qu"},{"full_name":"Glass, Bärbel","first_name":"Bärbel","last_name":"Glass"},{"first_name":"Michal","full_name":"Doležal, Michal","last_name":"Doležal"},{"full_name":"Schur, Florian","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur"},{"last_name":"Murciano","first_name":"Brice","full_name":"Murciano, Brice"},{"last_name":"Rein","first_name":"Alan","full_name":"Rein, Alan"},{"full_name":"Rumlová, Michaela","first_name":"Michaela","last_name":"Rumlová"},{"last_name":"Ruml","full_name":"Ruml, Tomáš","first_name":"Tomáš"},{"last_name":"Kräusslich","full_name":"Kräusslich, Hans-Georg","first_name":"Hans-Georg"},{"full_name":"Briggs, John A. G.","first_name":"John A. G.","last_name":"Briggs"}],"volume":115,"date_published":"2018-12-11T00:00:00Z","intvolume":"       115","_id":"5770","issue":"50","quality_controlled":"1","abstract":[{"text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.","lang":"eng"}],"date_created":"2018-12-20T21:09:37Z","publication_status":"published","external_id":{"isi":["000452866000022"],"pmid":["30478053"]},"scopus_import":"1","day":"11","publication":"Proceedings of the National Academy of Sciences","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1073/pnas.1811580115","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"oa":1,"pmid":1,"department":[{"_id":"FlSc"}],"year":"2018","title":"Structure and architecture of immature and mature murine leukemia virus capsids","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053","open_access":"1"}]}]