[{"month":"12","year":"2025","publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"article_type":"original","date_updated":"2026-01-05T08:32:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","date_created":"2026-01-04T23:01:36Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.molcel.2025.11.029","oa_version":"Published Version","author":[{"last_name":"Kelley","first_name":"Ron","full_name":"Kelley, Ron"},{"full_name":"Khavnekar, Sagar","first_name":"Sagar","last_name":"Khavnekar"},{"full_name":"Righetto, Ricardo D.","first_name":"Ricardo D.","last_name":"Righetto"},{"first_name":"Jessica","full_name":"Heebner, Jessica","last_name":"Heebner"},{"orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","full_name":"Obr, Martin","first_name":"Martin"},{"last_name":"Zhang","first_name":"Xianjun","full_name":"Zhang, Xianjun"},{"last_name":"Chakraborty","first_name":"Saikat","full_name":"Chakraborty, Saikat"},{"last_name":"Tagiltsev","first_name":"Grigory","full_name":"Tagiltsev, Grigory"},{"orcid":"0000-0002-6080-839X","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","full_name":"Michael, Alicia","first_name":"Alicia"},{"last_name":"Van Dorst","first_name":"Sofie","full_name":"Van Dorst, Sofie"},{"first_name":"Florent","full_name":"Waltz, Florent","last_name":"Waltz"},{"last_name":"Mccafferty","first_name":"Caitlyn L.","full_name":"Mccafferty, Caitlyn L."},{"first_name":"Lorenz","full_name":"Lamm, Lorenz","last_name":"Lamm"},{"full_name":"Zufferey, Simon","first_name":"Simon","last_name":"Zufferey"},{"full_name":"Van Der Stappen, Philippe","first_name":"Philippe","last_name":"Van Der Stappen"},{"full_name":"Van Den Hoek, Hugo","first_name":"Hugo","last_name":"Van Den Hoek"},{"last_name":"Wietrzynski","full_name":"Wietrzynski, Wojciech","first_name":"Wojciech"},{"last_name":"Harar","orcid":"0000-0001-5206-1794","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","first_name":"Pavol","full_name":"Harar, Pavol"},{"full_name":"Wan, William","first_name":"William","last_name":"Wan"},{"full_name":"Briggs, John A.G.","first_name":"John A.G.","last_name":"Briggs"},{"last_name":"Plitzko","full_name":"Plitzko, Jürgen M.","first_name":"Jürgen M."},{"full_name":"Engel, Benjamin D.","first_name":"Benjamin D.","last_name":"Engel"},{"full_name":"Kotecha, Abhay","first_name":"Abhay","last_name":"Kotecha"}],"title":"Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii","PlanS_conform":"1","publisher":"Elsevier","oa":1,"publication":"Molecular Cell","publication_status":"inpress","article_processing_charge":"Yes (in subscription journal)","_id":"20935","OA_place":"publisher","abstract":[{"lang":"eng","text":"In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient production and sharing of large-scale cryo-ET datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB) milling with recent advances in cryo-ET acquisition and processing to generate a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii, which we provide as a community resource to drive method development and inspire biological discovery. To assay data quality, we performed subtomogram averaging of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset as well as the promise of modern cryo-ET workflows and open data sharing to empower visual proteomics."}],"department":[{"_id":"AlMi"}],"ddc":["570"],"quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","date_published":"2025-12-19T00:00:00Z","day":"19","status":"public","acknowledgement":"Calculations were performed at the Max Planck Institute of Biochemistry and the Raven Supercomputer of the Max Planck Computing and Data Facility (MPCDF) in Garching, Germany; at the sciCORE (http://scicore.unibas.ch/) scientific computing center at the University of Basel, Switzerland; and at Thermo Fisher Scientific, in Eindhoven, the Netherlands. This work was supported by Thermo Fisher Scientific. All lamella preparations and tilt-series collections used in this work were conducted at Thermo Fisher R&D facilities in Brno and Eindhoven, utilizing Arctis and Krios microscopes. This work was also supported by the ERC consolidator grant “cryOcean” (fulfilled by the Swiss State Secretariat for Education, Research and Innovation, M822.00045) as well as a Swiss Nanoscience Institute PhD school grant to B.D.E. and P.V.d.S., an EMBO long-term postdoctoral fellowship (ALTF-383-2022) to G.T., an SNSF Postdoctoral Fellowship (project 210561) to F.W., a Boehringer Ingelheim Fonds fellowship to L.L., and by the Max Planck Society to J.A.G.B. and J.M.P.","citation":{"ista":"Kelley R, Khavnekar S, Righetto RD, Heebner J, Obr M, Zhang X, Chakraborty S, Tagiltsev G, Michael AK, Van Dorst S, Waltz F, Mccafferty CL, Lamm L, Zufferey S, Van Der Stappen P, Van Den Hoek H, Wietrzynski W, Harar P, Wan W, Briggs JAG, Plitzko JM, Engel BD, Kotecha A. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell.","apa":"Kelley, R., Khavnekar, S., Righetto, R. D., Heebner, J., Obr, M., Zhang, X., … Kotecha, A. (n.d.). Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">https://doi.org/10.1016/j.molcel.2025.11.029</a>","short":"R. Kelley, S. Khavnekar, R.D. Righetto, J. Heebner, M. Obr, X. Zhang, S. Chakraborty, G. Tagiltsev, A.K. Michael, S. Van Dorst, F. Waltz, C.L. Mccafferty, L. Lamm, S. Zufferey, P. Van Der Stappen, H. Van Den Hoek, W. Wietrzynski, P. Harar, W. Wan, J.A.G. Briggs, J.M. Plitzko, B.D. Engel, A. Kotecha, Molecular Cell (n.d.).","mla":"Kelley, Ron, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” <i>Molecular Cell</i>, Elsevier, doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">10.1016/j.molcel.2025.11.029</a>.","chicago":"Kelley, Ron, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin Obr, Xianjun Zhang, Saikat Chakraborty, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” <i>Molecular Cell</i>. Elsevier, n.d. <a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">https://doi.org/10.1016/j.molcel.2025.11.029</a>.","ieee":"R. Kelley <i>et al.</i>, “Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii,” <i>Molecular Cell</i>. Elsevier.","ama":"Kelley R, Khavnekar S, Righetto RD, et al. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. <i>Molecular Cell</i>. doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">10.1016/j.molcel.2025.11.029</a>"},"main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2025.11.029","open_access":"1"}],"type":"journal_article"},{"_id":"17884","isi":1,"project":[{"call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"},{"name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms","grant_number":"25762","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A"}],"OA_place":"publisher","publication":"Nature Structural & Molecular Biology","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001306564000001"],"oaworkid":["W4402316284"],"pmid":["39242978"]},"scopus_import":"1","file_date_updated":"2025-04-23T07:02:33Z","volume":32,"abstract":[{"lang":"eng","text":"Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron tomography studies of HTLV-1 virus-like particles assembled in vitro, as well as derived from cells. This work shows that HTLV-1 uses a distinct mechanism of Gag–Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature capsid (CA) tubular arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal domain of CA. Mutagenesis analysis supports this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the C-terminal domain of CA. These results provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus and this helps explain why HTLV-1 particles are morphologically distinct."}],"department":[{"_id":"FlSc"},{"_id":"LeSa"}],"ddc":["570"],"pmid":1,"citation":{"ama":"Obr M, Percipalle M, Chernikova D, et al. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. <i>Nature Structural &#38; Molecular Biology</i>. 2025;32:268-276. doi:<a href=\"https://doi.org/10.1038/s41594-024-01390-8\">10.1038/s41594-024-01390-8</a>","ieee":"M. Obr <i>et al.</i>, “Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32. Springer Nature, pp. 268–276, 2025.","chicago":"Obr, Martin, Mathias Percipalle, Darya Chernikova, Huixin Yang, Andreas Thader, Gergely Pinke, Darío Porley Esteves, Louis M. Mansky, Robert A. Dick, and Florian KM Schur. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41594-024-01390-8\">https://doi.org/10.1038/s41594-024-01390-8</a>.","mla":"Obr, Martin, et al. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32, Springer Nature, 2025, pp. 268–76, doi:<a href=\"https://doi.org/10.1038/s41594-024-01390-8\">10.1038/s41594-024-01390-8</a>.","short":"M. Obr, M. Percipalle, D. Chernikova, H. Yang, A. Thader, G. Pinke, D. Porley Esteves, L.M. Mansky, R.A. Dick, F.K. Schur, Nature Structural &#38; Molecular Biology 32 (2025) 268–276.","apa":"Obr, M., Percipalle, M., Chernikova, D., Yang, H., Thader, A., Pinke, G., … Schur, F. K. (2025). Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01390-8\">https://doi.org/10.1038/s41594-024-01390-8</a>","ista":"Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley Esteves D, Mansky LM, Dick RA, Schur FK. 2025. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Nature Structural &#38; Molecular Biology. 32, 268–276."},"acknowledgement":"This work was funded by the Institute of Science and Technology Austria (ISTA) and the Austrian Science Fund (grant P31445 to F.K.M.S.). Access to high-resolution cryo-ET data acquisition at European Molecular Biology Laboratory (EMBL) Heidelberg was supported through the EMBL cryo-EM platform. We thank V.-V. Hodirnau at ISTA and W. Hagen and F. Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This research was also supported by the scientific service units of ISTA through resources provided by Scientific Computing, the Life Science Facility, and the EM Facility. L.M.M. was supported by National Institutes of Health grants R01 GM151775 and R21 DE032878 and by the University of Minnesota Masonic Cancer Center. D.P. was supported by the DOC doctoral fellowship program of the Austrian Academy of Sciences. R.A.D was supported by the National Institute of Allergy and Infectious Diseases (grant R01AI147890). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Specifically, we also want to thank A. Schlögl for computational support and J. Hansen and V. Vogt for critical comments on the manuscript. We also thank the other members of the Schur lab for helpful discussions and experimental advice.","date_published":"2025-02-01T00:00:00Z","day":"01","APC_amount":"12348 EUR","status":"public","type":"journal_article","intvolume":"        32","year":"2025","file":[{"content_type":"application/pdf","file_size":13724041,"success":1,"access_level":"open_access","creator":"dernst","file_name":"2025_NatureStrucBio_Obr.pdf","checksum":"c641ad94afb28917b20425db676fc3ee","date_created":"2025-04-23T07:02:33Z","file_id":"19608","relation":"main_file","date_updated":"2025-04-23T07:02:33Z"}],"article_type":"original","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"has_accepted_license":"1","month":"02","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","date_updated":"2026-03-16T12:55:18Z","oaworkid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","date_created":"2024-09-08T10:29:06Z","oa_version":"Published Version","author":[{"full_name":"Obr, Martin","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","last_name":"Obr"},{"full_name":"Percipalle, Mathias","first_name":"Mathias","id":"4986e21c-eb97-11eb-a6c2-a4ef0b629971","last_name":"Percipalle"},{"first_name":"Darya","full_name":"Chernikova, Darya","last_name":"Chernikova","id":"7dbaf460-fa9e-11eb-b0ca-bc7c7ff21ad0"},{"first_name":"Huixin","full_name":"Yang, Huixin","last_name":"Yang"},{"id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","last_name":"Thader","full_name":"Thader, Andreas","first_name":"Andreas"},{"id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","last_name":"Pinke","full_name":"Pinke, Gergely","first_name":"Gergely"},{"first_name":"Dario J","full_name":"Porley, Dario J","last_name":"Porley","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mansky","full_name":"Mansky, Louis M.","first_name":"Louis M."},{"last_name":"Dick","first_name":"Robert A.","full_name":"Dick, Robert A."},{"full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"}],"title":"Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice","page":"268-276","doi":"10.1038/s41594-024-01390-8","oa":1,"publisher":"Springer Nature"},{"doi":"10.1371/journal.ppat.1011562","oa_version":"Published Version","title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells","author":[{"last_name":"Koch","first_name":"Jana","full_name":"Koch, Jana"},{"full_name":"Xin, Qilin","first_name":"Qilin","last_name":"Xin"},{"last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","first_name":"Martin","full_name":"Obr, Martin"},{"last_name":"Schäfer","first_name":"Alicia","full_name":"Schäfer, Alicia"},{"last_name":"Rolfs","full_name":"Rolfs, Nina","first_name":"Nina"},{"last_name":"Anagho","full_name":"Anagho, Holda A.","first_name":"Holda A."},{"last_name":"Kudulyte","first_name":"Aiste","full_name":"Kudulyte, Aiste"},{"full_name":"Woltereck, Lea","first_name":"Lea","last_name":"Woltereck"},{"last_name":"Kummer","first_name":"Susann","full_name":"Kummer, Susann"},{"last_name":"Campos","full_name":"Campos, Joaquin","first_name":"Joaquin"},{"last_name":"Uckeley","full_name":"Uckeley, Zina M.","first_name":"Zina M."},{"last_name":"Bell-Sakyi","first_name":"Lesley","full_name":"Bell-Sakyi, Lesley"},{"full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg","last_name":"Kräusslich"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian Km","full_name":"Schur, Florian Km"},{"last_name":"Acuna","full_name":"Acuna, Claudio","first_name":"Claudio"},{"full_name":"Lozach, Pierre Yves","first_name":"Pierre Yves","last_name":"Lozach"}],"publisher":"Public Library of Science","oa":1,"month":"08","year":"2023","article_type":"original","acknowledged_ssus":[{"_id":"EM-Fac"}],"has_accepted_license":"1","publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"file":[{"date_updated":"2023-09-06T06:41:52Z","file_id":"14269","relation":"main_file","date_created":"2023-09-06T06:41:52Z","checksum":"47ca3bb54b27f28b05644be0ad064bc6","file_name":"2023_PloSPathogens_Koch.pdf","creator":"dernst","access_level":"open_access","success":1,"file_size":4458336,"content_type":"application/pdf"}],"date_updated":"2025-04-15T08:24:50Z","date_created":"2023-09-03T22:01:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"14","article_number":"e1011562","date_published":"2023-08-14T00:00:00Z","status":"public","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.","citation":{"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.","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>","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>","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."},"intvolume":"        19","type":"journal_article","publication":"PLoS Pathogens","publication_status":"published","article_processing_charge":"Yes","issue":"8","_id":"14255","project":[{"call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445"}],"isi":1,"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"}],"file_date_updated":"2023-09-06T06:41:52Z","volume":19,"pmid":1,"ddc":["570"],"department":[{"_id":"FlSc"}],"language":[{"iso":"eng"}],"quality_controlled":"1","external_id":{"isi":["001050846300004"],"pmid":["37578957"]},"scopus_import":"1"},{"date_updated":"2025-04-15T08:24:49Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["virology","insect science","immunology","microbiology"],"date_created":"2022-01-18T10:04:18Z","year":"2022","article_type":"original","publication_identifier":{"eissn":["1098-5514"],"issn":["0022-538X"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"03","publisher":"American Society for Microbiology","oa":1,"oa_version":"Published Version","author":[{"first_name":"Stefan","full_name":"Windhaber, Stefan","last_name":"Windhaber"},{"full_name":"Xin, Qilin","first_name":"Qilin","last_name":"Xin"},{"full_name":"Uckeley, Zina M.","first_name":"Zina M.","last_name":"Uckeley"},{"full_name":"Koch, Jana","first_name":"Jana","last_name":"Koch"},{"first_name":"Martin","full_name":"Obr, Martin","last_name":"Obr","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Garnier","full_name":"Garnier, Céline","first_name":"Céline"},{"first_name":"Catherine","full_name":"Luengo-Guyonnot, Catherine","last_name":"Luengo-Guyonnot"},{"last_name":"Duboeuf","full_name":"Duboeuf, Maëva","first_name":"Maëva"},{"full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"},{"last_name":"Lozach","full_name":"Lozach, Pierre-Yves","first_name":"Pierre-Yves"}],"title":"The Orthobunyavirus Germiston enters host cells from late endosomes","doi":"10.1128/jvi.02146-21","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000779305000033"],"pmid":["35019710"]},"scopus_import":"1","volume":96,"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"}],"department":[{"_id":"FlSc"}],"pmid":1,"_id":"10639","isi":1,"project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"publication_status":"published","publication":"Journal of Virology","issue":"5","article_processing_charge":"No","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8906410","open_access":"1"}],"type":"journal_article","intvolume":"        96","citation":{"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>","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.","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.","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>","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>.","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).","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>."},"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.","date_published":"2022-03-01T00:00:00Z","day":"01","article_number":"e02146-21","status":"public"},{"citation":{"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>","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.","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>.","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>.","short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022).","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>","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."},"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.","status":"public","date_published":"2022-06-01T00:00:00Z","day":"01","article_number":"107852","type":"journal_article","intvolume":"       214","isi":1,"project":[{"call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"}],"_id":"11155","issue":"2","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Structural Biology","publication_status":"published","external_id":{"isi":["000790733600001"],"pmid":["35351542"]},"scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"ddc":["570"],"department":[{"_id":"FlSc"}],"pmid":1,"file_date_updated":"2022-08-02T11:07:58Z","volume":214,"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"}],"author":[{"last_name":"Obr","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Obr, Martin"},{"last_name":"Hagen","first_name":"Wim J.H.","full_name":"Hagen, Wim J.H."},{"first_name":"Robert A.","full_name":"Dick, Robert A.","last_name":"Dick"},{"last_name":"Yu","first_name":"Lingbo","full_name":"Yu, Lingbo"},{"first_name":"Abhay","full_name":"Kotecha, Abhay","last_name":"Kotecha"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM"}],"title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs","oa_version":"Published Version","doi":"10.1016/j.jsb.2022.107852","publisher":"Elsevier","oa":1,"file":[{"success":1,"access_level":"open_access","content_type":"application/pdf","file_size":7080863,"creator":"dernst","checksum":"0b1eb53447aae8e95ae4c12d193b0b00","file_name":"2022_JourStructuralBiology_Obr.pdf","relation":"main_file","file_id":"11722","date_updated":"2022-08-02T11:07:58Z","date_created":"2022-08-02T11:07:58Z"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"article_type":"original","has_accepted_license":"1","publication_identifier":{"issn":["1047-8477"]},"year":"2022","month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["Structural Biology"],"date_created":"2022-04-15T07:10:26Z","corr_author":"1","date_updated":"2025-04-15T08:24:50Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","date_updated":"2025-04-15T08:24:49Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-10-07T09:13:29Z","keyword":["virology","infectious diseases"],"year":"2021","file":[{"date_created":"2021-10-08T10:38:15Z","date_updated":"2021-10-08T10:38:15Z","relation":"main_file","file_id":"10115","file_name":"2021_Viruses_Obr.pdf","checksum":"bcfd72a12977d48e22df3d0cc55aacf1","creator":"cchlebak","file_size":4146796,"content_type":"application/pdf","access_level":"open_access","success":1}],"publication_identifier":{"issn":["1999-4915"]},"has_accepted_license":"1","article_type":"original","month":"09","oa":1,"publisher":"MDPI","oa_version":"Published Version","author":[{"orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","full_name":"Obr, Martin","first_name":"Martin"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM"},{"last_name":"Dick","full_name":"Dick, Robert A.","first_name":"Robert A."}],"title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly","doi":"10.3390/v13091853","quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","external_id":{"isi":["000699841100001"],"pmid":["34578434"]},"file_date_updated":"2021-10-08T10:38:15Z","volume":13,"abstract":[{"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.","lang":"eng"}],"ddc":["616"],"department":[{"_id":"FlSc"}],"pmid":1,"_id":"10103","isi":1,"project":[{"call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"}],"publication_status":"published","publication":"Viruses","issue":"9","article_processing_charge":"Yes","type":"journal_article","intvolume":"        13","acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","citation":{"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>.","short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).","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>.","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.","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>","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.","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>"},"date_published":"2021-09-17T00:00:00Z","article_number":"1853","day":"17","status":"public"},{"year":"2021","file":[{"file_size":6166295,"content_type":"application/pdf","access_level":"open_access","success":1,"creator":"kschuh","file_name":"2021_NatureCommunications_Obr.pdf","checksum":"53ccc53d09a9111143839dbe7784e663","date_created":"2021-06-09T15:21:14Z","date_updated":"2021-06-09T15:21:14Z","relation":"main_file","file_id":"9538"}],"publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"has_accepted_license":"1","month":"05","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","date_updated":"2025-04-15T08:24:49Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"date_created":"2021-05-28T14:25:50Z","oa_version":"Published Version","author":[{"id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","last_name":"Obr","full_name":"Obr, Martin","first_name":"Martin"},{"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"},{"first_name":"Marco","full_name":"Klanschnig, Marco","last_name":"Klanschnig"},{"last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Thader, Andreas"},{"last_name":"Johnson","full_name":"Johnson, Marc C.","first_name":"Marc C."},{"last_name":"Vogt","full_name":"Vogt, Volker M.","first_name":"Volker M."},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM"},{"first_name":"Robert A.","full_name":"Dick, Robert A.","last_name":"Dick"}],"title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","doi":"10.1038/s41467-021-23506-0","publisher":"Nature Research","oa":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/","description":"News on IST Homepage"}]},"_id":"9431","isi":1,"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"publication":"Nature Communications","publication_status":"published","issue":"1","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000659145000011"]},"scopus_import":"1","file_date_updated":"2021-06-09T15:21:14Z","volume":12,"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"}],"department":[{"_id":"FlSc"}],"ddc":["570"],"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).","citation":{"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>.","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).","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>.","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>","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.","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.","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>"},"date_published":"2021-05-28T00:00:00Z","day":"28","article_number":"3226","status":"public","type":"journal_article","intvolume":"        12"},{"doi":"10.1038/s41467-020-14535-2","oa_version":"Published Version","title":"Benchmarking tomographic acquisition schemes for high-resolution structural biology","author":[{"full_name":"Turoňová, Beata","first_name":"Beata","last_name":"Turoňová"},{"full_name":"Hagen, Wim J.H.","first_name":"Wim J.H.","last_name":"Hagen"},{"first_name":"Martin","full_name":"Obr, Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564"},{"full_name":"Mosalaganti, Shyamal","first_name":"Shyamal","last_name":"Mosalaganti"},{"last_name":"Beugelink","first_name":"J. Wouter","full_name":"Beugelink, J. Wouter"},{"first_name":"Christian E.","full_name":"Zimmerli, Christian E.","last_name":"Zimmerli"},{"first_name":"Hans Georg","full_name":"Kräusslich, Hans Georg","last_name":"Kräusslich"},{"full_name":"Beck, Martin","first_name":"Martin","last_name":"Beck"}],"publisher":"Springer Nature","oa":1,"month":"02","year":"2020","publication_identifier":{"eissn":["2041-1723"]},"has_accepted_license":"1","article_type":"original","file":[{"file_name":"2020_NatureComm_Turonova.pdf","checksum":"2c8d10475e1b0d397500760e28bdf561","date_created":"2020-02-24T14:00:54Z","date_updated":"2020-07-14T12:47:59Z","relation":"main_file","file_id":"7517","file_size":2027529,"content_type":"application/pdf","access_level":"open_access","creator":"dernst"}],"date_updated":"2026-04-03T09:27:26Z","date_created":"2020-02-23T23:00:35Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"13","article_number":"876","date_published":"2020-02-13T00:00:00Z","status":"public","citation":{"ama":"Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>","ieee":"B. Turoňová <i>et al.</i>, “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Turoňová, Beata, Wim J.H. Hagen, Martin Obr, Shyamal Mosalaganti, J. Wouter Beugelink, Christian E. Zimmerli, Hans Georg Kräusslich, and Martin Beck. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>.","mla":"Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” <i>Nature Communications</i>, vol. 11, 876, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>.","short":"B. Turoňová, W.J.H. Hagen, M. Obr, S. Mosalaganti, J.W. Beugelink, C.E. Zimmerli, H.G. Kräusslich, M. Beck, Nature Communications 11 (2020).","apa":"Turoňová, B., Hagen, W. J. H., Obr, M., Mosalaganti, S., Beugelink, J. W., Zimmerli, C. E., … Beck, M. (2020). Benchmarking tomographic acquisition schemes for high-resolution structural biology. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>","ista":"Turoňová B, Hagen WJH, Obr M, Mosalaganti S, Beugelink JW, Zimmerli CE, Kräusslich HG, Beck M. 2020. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 11, 876."},"intvolume":"        11","type":"journal_article","publication_status":"published","publication":"Nature Communications","article_processing_charge":"No","_id":"7511","isi":1,"abstract":[{"text":"Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.","lang":"eng"}],"volume":11,"file_date_updated":"2020-07-14T12:47:59Z","pmid":1,"department":[{"_id":"FlSc"}],"ddc":["570"],"language":[{"iso":"eng"}],"quality_controlled":"1","scopus_import":"1","external_id":{"isi":["000514928000017"],"pmid":["32054835"]}},{"isi":1,"_id":"6890","article_processing_charge":"No","publication_status":"published","publication":"Complementary Strategies to Study Virus Structure and Function","external_id":{"isi":["000501594500006"],"pmid":["    31522703"]},"scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"FlSc"}],"pmid":1,"volume":105,"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."}],"citation":{"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>","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.","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>","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.","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>.","short":"M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function, Elsevier, 2019, pp. 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>."},"status":"public","date_published":"2019-08-27T00:00:00Z","day":"27","type":"book_chapter","intvolume":"       105","publication_identifier":{"issn":["0065-3527"],"isbn":["9780128184561"]},"year":"2019","month":"08","series_title":"Advances in Virus Research","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-09-18T08:15:37Z","date_updated":"2023-08-30T06:56:00Z","author":[{"first_name":"Martin","full_name":"Obr, Martin","last_name":"Obr","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM"}],"title":"Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging","editor":[{"first_name":"Félix A.","full_name":"Rey, Félix A.","last_name":"Rey"}],"oa_version":"None","doi":"10.1016/bs.aivir.2019.07.008","page":"117-159","publisher":"Elsevier"},{"year":"2016","_id":"816","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","month":"07","article_processing_charge":"No","language":[{"iso":"eng"}],"external_id":{"pmid":["27417497"]},"scopus_import":"1","extern":"1","volume":353,"abstract":[{"text":"Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs.We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- And intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease.We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1.","lang":"eng"}],"date_updated":"2026-05-20T07:41:16Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2018-12-11T11:48:39Z","pmid":1,"acknowledgement":"The authors thank B. Glass for preparation of the immature HIV-1 (D25A) sample; J. Plitzko and D. Tegunov for providing the K2Align software; and S. Mattei, N. Hoffman, F. Thommen, A. Sonnen, and S. Dodonova for technical assistance and/or discussion. This study was supported by Deutsche Forschungsgemeinschaft grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1 (to H.-G.K.). The Briggs laboratory acknowledges financial support from the European Molecular Biology Laboratory (EMBL) and from the Chica und Heinz Schaller Stiftung. W.W. was supported by a European Molecular Biology Organization Long-Term Fellowship (ALTF 748-2014). A.J.J. acknowledges support by the EMBL Interdisciplinary Postdoc Program under the Marie Curie Action COFUND (PCOFUND-GA-2008-229597) and by the Joachim Herz Stiftung. This study was technically supported by the EMBL information technology services unit and the EMBL Proteomics Core Facility. F.K.M.S., M.O., H.-G.K., and J.A.G.B. designed the experiments, with J.M.K. assisting in the design of those involving mass spectrometry. F.K.M.S. and M.O. prepared samples. W.J.H.H. implemented tomography acquisition schemes. F.K.M.S. and W.J.H.H. acquired the data. F.K.M.S. and W.W. processed images. F.K.M.S., A.J.J., and C.S. refined the model. F.K.M.S., M.O., and J.A.G.B. analyzed the data. F.K.M.S. and J.A.G.B. wrote the manuscript with support from all authors. Representative tomograms and the final electron microscopy structures have been deposited in the Electron Microscopy Data Bank with accession numbers EMD-4015, EMD-4016, EMD-4017, EMD-4018, EMD-4019, and EMD-4020. The refined HIV-1 CA-SP1 model has been deposited in the Protein Data Bank with accession number 5L93.","oa_version":"None","citation":{"ieee":"F. K. Schur <i>et al.</i>, <i>An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation</i>, vol. 353. American Association for the Advancement of Science, 2016, pp. 506–508.","ama":"Schur FK, Obr M, Hagen W, et al. <i>An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation</i>. Vol 353. American Association for the Advancement of Science; 2016:506-508. doi:<a href=\"https://doi.org/10.1126/science.aaf9620\">10.1126/science.aaf9620</a>","short":"F.K. Schur, M. Obr, W. Hagen, W. Wan, A. Jakobi, J. Kirkpatrick, C. Sachse, H. Kraüsslich, J. Briggs, An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation, American Association for the Advancement of Science, 2016.","mla":"Schur, Florian KM, et al. <i>An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation</i>. Vol. 353, American Association for the Advancement of Science, 2016, pp. 506–08, doi:<a href=\"https://doi.org/10.1126/science.aaf9620\">10.1126/science.aaf9620</a>.","chicago":"Schur, Florian KM, Martin Obr, Wim Hagen, William Wan, Arjen Jakobi, Joanna Kirkpatrick, Carsten Sachse, Hans Kraüsslich, and John Briggs. <i>An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation</i>. Vol. 353. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/science.aaf9620\">https://doi.org/10.1126/science.aaf9620</a>.","apa":"Schur, F. K., Obr, M., Hagen, W., Wan, W., Jakobi, A., Kirkpatrick, J., … Briggs, J. (2016). <i>An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation</i> (Vol. 353, pp. 506–508). American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf9620\">https://doi.org/10.1126/science.aaf9620</a>","ista":"Schur FK, Obr M, Hagen W, Wan W, Jakobi A, Kirkpatrick J, Sachse C, Kraüsslich H, Briggs J. 2016. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation, American Association for the Advancement of Science,p."},"author":[{"last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Schur, Florian"},{"last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","first_name":"Martin","full_name":"Obr, Martin"},{"last_name":"Hagen","full_name":"Hagen, Wim","first_name":"Wim"},{"last_name":"Wan","full_name":"Wan, William","first_name":"William"},{"last_name":"Jakobi","first_name":"Arjen","full_name":"Jakobi, Arjen"},{"first_name":"Joanna","full_name":"Kirkpatrick, Joanna","last_name":"Kirkpatrick"},{"full_name":"Sachse, Carsten","first_name":"Carsten","last_name":"Sachse"},{"first_name":"Hans","full_name":"Kraüsslich, Hans","last_name":"Kraüsslich"},{"last_name":"Briggs","full_name":"Briggs, John","first_name":"John"}],"title":"An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation","publist_id":"6834","date_published":"2016-07-29T00:00:00Z","page":"506 - 508","day":"29","doi":"10.1126/science.aaf9620","status":"public","publisher":"American Association for the Advancement of Science","type":"report","intvolume":"       353"}]