--- _id: '14255' abstract: - lang: eng 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. acknowledged_ssus: - _id: EM-Fac 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." article_number: e1011562 article_processing_charge: Yes article_type: original author: - first_name: Jana full_name: Koch, Jana last_name: Koch - first_name: Qilin full_name: Xin, Qilin last_name: Xin - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Alicia full_name: Schäfer, Alicia last_name: Schäfer - first_name: Nina full_name: Rolfs, Nina last_name: Rolfs - first_name: Holda A. full_name: Anagho, Holda A. last_name: Anagho - first_name: Aiste full_name: Kudulyte, Aiste last_name: Kudulyte - first_name: Lea full_name: Woltereck, Lea last_name: Woltereck - first_name: Susann full_name: Kummer, Susann last_name: Kummer - first_name: Joaquin full_name: Campos, Joaquin last_name: Campos - first_name: Zina M. full_name: Uckeley, Zina M. last_name: Uckeley - first_name: Lesley full_name: Bell-Sakyi, Lesley last_name: Bell-Sakyi - first_name: Hans Georg full_name: Kräusslich, Hans Georg last_name: Kräusslich - first_name: Florian Km full_name: Schur, Florian Km id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Claudio full_name: Acuna, Claudio last_name: Acuna - first_name: Pierre Yves full_name: Lozach, Pierre Yves last_name: Lozach citation: ama: Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 2023;19(8). doi:10.1371/journal.ppat.1011562 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. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1011562 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.” PLoS Pathogens. Public Library of Science, 2023. https://doi.org/10.1371/journal.ppat.1011562. ieee: J. Koch et al., “The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells,” PLoS Pathogens, vol. 19, no. 8. Public Library of Science, 2023. 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. mla: Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:10.1371/journal.ppat.1011562. 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). date_created: 2023-09-03T22:01:14Z date_published: 2023-08-14T00:00:00Z date_updated: 2023-12-13T12:22:22Z day: '14' ddc: - '570' department: - _id: FlSc doi: 10.1371/journal.ppat.1011562 external_id: isi: - '001050846300004' pmid: - '37578957' file: - access_level: open_access checksum: 47ca3bb54b27f28b05644be0ad064bc6 content_type: application/pdf creator: dernst date_created: 2023-09-06T06:41:52Z date_updated: 2023-09-06T06:41:52Z file_id: '14269' file_name: 2023_PloSPathogens_Koch.pdf file_size: 4458336 relation: main_file success: 1 file_date_updated: 2023-09-06T06:41:52Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: PLoS Pathogens publication_identifier: eissn: - 1553-7374 issn: - 1553-7366 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2023' ... --- _id: '10639' abstract: - lang: eng 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. acknowledged_ssus: - _id: EM-Fac 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. article_number: e02146-21 article_processing_charge: No article_type: original author: - first_name: Stefan full_name: Windhaber, Stefan last_name: Windhaber - first_name: Qilin full_name: Xin, Qilin last_name: Xin - first_name: Zina M. full_name: Uckeley, Zina M. last_name: Uckeley - first_name: Jana full_name: Koch, Jana last_name: Koch - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr - first_name: Céline full_name: Garnier, Céline last_name: Garnier - first_name: Catherine full_name: Luengo-Guyonnot, Catherine last_name: Luengo-Guyonnot - first_name: Maëva full_name: Duboeuf, Maëva last_name: Duboeuf - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Pierre-Yves full_name: Lozach, Pierre-Yves last_name: Lozach citation: ama: Windhaber S, Xin Q, Uckeley ZM, et al. The Orthobunyavirus Germiston enters host cells from late endosomes. Journal of Virology. 2022;96(5). doi:10.1128/jvi.02146-21 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. Journal of Virology. American Society for Microbiology. https://doi.org/10.1128/jvi.02146-21 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.” Journal of Virology. American Society for Microbiology, 2022. https://doi.org/10.1128/jvi.02146-21. ieee: S. Windhaber et al., “The Orthobunyavirus Germiston enters host cells from late endosomes,” Journal of Virology, vol. 96, no. 5. American Society for Microbiology, 2022. 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. mla: Windhaber, Stefan, et al. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.” Journal of Virology, vol. 96, no. 5, e02146-21, American Society for Microbiology, 2022, doi:10.1128/jvi.02146-21. 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). date_created: 2022-01-18T10:04:18Z date_published: 2022-03-01T00:00:00Z date_updated: 2023-08-02T13:52:33Z day: '01' department: - _id: FlSc doi: 10.1128/jvi.02146-21 external_id: isi: - '000779305000033' pmid: - '35019710' intvolume: ' 96' isi: 1 issue: '5' keyword: - virology - insect science - immunology - microbiology language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8906410 month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: Journal of Virology publication_identifier: eissn: - 1098-5514 issn: - 0022-538X publication_status: published publisher: American Society for Microbiology quality_controlled: '1' scopus_import: '1' status: public title: The Orthobunyavirus Germiston enters host cells from late endosomes type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 96 year: '2022' ... --- _id: '11155' abstract: - lang: eng 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. acknowledged_ssus: - _id: LifeSc - _id: ScienComp - _id: EM-Fac 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. article_number: '107852' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr - first_name: Wim J.H. full_name: Hagen, Wim J.H. last_name: Hagen - first_name: Robert A. full_name: Dick, Robert A. last_name: Dick - first_name: Lingbo full_name: Yu, Lingbo last_name: Yu - first_name: Abhay full_name: Kotecha, Abhay last_name: Kotecha - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 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. Journal of Structural Biology. 2022;214(2). doi:10.1016/j.jsb.2022.107852 apa: Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., & Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2022.107852 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.” Journal of Structural Biology. Elsevier, 2022. https://doi.org/10.1016/j.jsb.2022.107852. 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,” Journal of Structural Biology, vol. 214, no. 2. Elsevier, 2022. 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. mla: Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” Journal of Structural Biology, vol. 214, no. 2, 107852, Elsevier, 2022, doi:10.1016/j.jsb.2022.107852. short: M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022). date_created: 2022-04-15T07:10:26Z date_published: 2022-06-01T00:00:00Z date_updated: 2023-08-03T06:25:23Z day: '01' ddc: - '570' department: - _id: FlSc doi: 10.1016/j.jsb.2022.107852 external_id: isi: - '000790733600001' pmid: - '35351542' file: - access_level: open_access checksum: 0b1eb53447aae8e95ae4c12d193b0b00 content_type: application/pdf creator: dernst date_created: 2022-08-02T11:07:58Z date_updated: 2022-08-02T11:07:58Z file_id: '11722' file_name: 2022_JourStructuralBiology_Obr.pdf file_size: 7080863 relation: main_file success: 1 file_date_updated: 2022-08-02T11:07:58Z has_accepted_license: '1' intvolume: ' 214' isi: 1 issue: '2' keyword: - Structural Biology language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: Journal of Structural Biology publication_identifier: issn: - 1047-8477 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 214 year: '2022' ... --- _id: '9431' abstract: - lang: eng 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. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: EM-Fac 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). article_number: '3226' article_processing_charge: No article_type: original author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr - first_name: Clifton L. full_name: Ricana, Clifton L. last_name: Ricana - first_name: Nadia full_name: Nikulin, Nadia last_name: Nikulin - first_name: Jon-Philip R. full_name: Feathers, Jon-Philip R. last_name: Feathers - first_name: Marco full_name: Klanschnig, Marco last_name: Klanschnig - first_name: Andreas full_name: Thader, Andreas id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87 last_name: Thader - first_name: Marc C. full_name: Johnson, Marc C. last_name: Johnson - first_name: Volker M. full_name: Vogt, Volker M. last_name: Vogt - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Robert A. full_name: Dick, Robert A. last_name: Dick citation: 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. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0 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. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-23506-0 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.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0. ieee: M. Obr et al., “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications, 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. 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.” Nature Communications, vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0. 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). date_created: 2021-05-28T14:25:50Z date_published: 2021-05-28T00:00:00Z date_updated: 2023-08-08T13:53:53Z day: '28' ddc: - '570' department: - _id: FlSc doi: 10.1038/s41467-021-23506-0 external_id: isi: - '000659145000011' file: - access_level: open_access checksum: 53ccc53d09a9111143839dbe7784e663 content_type: application/pdf creator: kschuh date_created: 2021-06-09T15:21:14Z date_updated: 2021-06-09T15:21:14Z file_id: '9538' file_name: 2021_NatureCommunications_Obr.pdf file_size: 6166295 relation: main_file success: 1 file_date_updated: 2021-06-09T15:21:14Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Nature Research quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/how-retroviruses-become-infectious/ scopus_import: '1' status: public title: Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10103' 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. acknowledgement: We thank Volker M. Vogt for his critical comments in preparation of the review. article_number: '1853' article_processing_charge: Yes article_type: original author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Robert A. full_name: Dick, Robert A. last_name: Dick citation: ama: Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 2021;13(9). doi:10.3390/v13091853 apa: Obr, M., Schur, F. K., & Dick, R. A. (2021). A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. MDPI. https://doi.org/10.3390/v13091853 chicago: Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses. MDPI, 2021. https://doi.org/10.3390/v13091853. ieee: M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role of IP6 in immature and mature retroviral assembly,” Viruses, vol. 13, no. 9. MDPI, 2021. 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. mla: Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses, vol. 13, no. 9, 1853, MDPI, 2021, doi:10.3390/v13091853. short: M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021). date_created: 2021-10-07T09:13:29Z date_published: 2021-09-17T00:00:00Z date_updated: 2023-08-14T07:21:51Z day: '17' ddc: - '616' department: - _id: FlSc doi: 10.3390/v13091853 external_id: isi: - '000699841100001' pmid: - '34578434' file: - access_level: open_access checksum: bcfd72a12977d48e22df3d0cc55aacf1 content_type: application/pdf creator: cchlebak date_created: 2021-10-08T10:38:15Z date_updated: 2021-10-08T10:38:15Z file_id: '10115' file_name: 2021_Viruses_Obr.pdf file_size: 4146796 relation: main_file success: 1 file_date_updated: 2021-10-08T10:38:15Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '9' keyword: - virology - infectious diseases language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: Viruses publication_identifier: issn: - 1999-4915 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: A structural perspective of the role of IP6 in immature and mature retroviral assembly tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2021' ... --- _id: '7511' abstract: - lang: eng 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. article_number: '876' article_processing_charge: No article_type: original author: - first_name: Beata full_name: Turoňová, Beata last_name: Turoňová - first_name: Wim J.H. full_name: Hagen, Wim J.H. last_name: Hagen - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Shyamal full_name: Mosalaganti, Shyamal last_name: Mosalaganti - first_name: J. Wouter full_name: Beugelink, J. Wouter last_name: Beugelink - first_name: Christian E. full_name: Zimmerli, Christian E. last_name: Zimmerli - first_name: Hans Georg full_name: Kräusslich, Hans Georg last_name: Kräusslich - first_name: Martin full_name: Beck, Martin last_name: Beck citation: ama: Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 2020;11. doi:10.1038/s41467-020-14535-2 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. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-14535-2 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.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-14535-2. ieee: B. Turoňová et al., “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” Nature Communications, vol. 11. Springer Nature, 2020. 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. mla: Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” Nature Communications, vol. 11, 876, Springer Nature, 2020, doi:10.1038/s41467-020-14535-2. 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). date_created: 2020-02-23T23:00:35Z date_published: 2020-02-13T00:00:00Z date_updated: 2023-08-18T06:36:41Z day: '13' ddc: - '570' department: - _id: FlSc doi: 10.1038/s41467-020-14535-2 external_id: isi: - '000514928000017' file: - access_level: open_access checksum: 2c8d10475e1b0d397500760e28bdf561 content_type: application/pdf creator: dernst date_created: 2020-02-24T14:00:54Z date_updated: 2020-07-14T12:47:59Z file_id: '7517' file_name: 2020_NatureComm_Turonova.pdf file_size: 2027529 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Benchmarking tomographic acquisition schemes for high-resolution structural biology tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '6890' 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. article_processing_charge: No author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: 'Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. Complementary Strategies to Study Virus Structure and Function. Vol 105. Advances in Virus Research. Elsevier; 2019:117-159. doi:10.1016/bs.aivir.2019.07.008' apa: Obr, M., & Schur, F. K. (2019). Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In F. A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function (Vol. 105, pp. 117–159). Elsevier. https://doi.org/10.1016/bs.aivir.2019.07.008 chicago: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” In Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. https://doi.org/10.1016/bs.aivir.2019.07.008. ieee: M. Obr and F. K. Schur, “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, F. A. Rey, Ed. Elsevier, 2019, pp. 117–159. 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.” Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:10.1016/bs.aivir.2019.07.008. short: M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function, Elsevier, 2019, pp. 117–159. date_created: 2019-09-18T08:15:37Z date_published: 2019-08-27T00:00:00Z date_updated: 2023-08-30T06:56:00Z day: '27' department: - _id: FlSc doi: 10.1016/bs.aivir.2019.07.008 editor: - first_name: Félix A. full_name: Rey, Félix A. last_name: Rey external_id: isi: - '000501594500006' pmid: - ' 31522703' intvolume: ' 105' isi: 1 language: - iso: eng month: '08' oa_version: None page: 117-159 pmid: 1 publication: Complementary Strategies to Study Virus Structure and Function publication_identifier: isbn: - '9780128184561' issn: - 0065-3527 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' series_title: Advances in Virus Research status: public title: Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging type: book_chapter user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 105 year: '2019' ... --- _id: '816' abstract: - lang: eng 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. 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. author: - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Martin full_name: Martin Obr id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr - first_name: Wim full_name: Hagen, Wim J last_name: Hagen - first_name: William full_name: Wan, William last_name: Wan - first_name: Arjen full_name: Jakobi, Arjen J last_name: Jakobi - first_name: Joanna full_name: Kirkpatrick, Joanna M last_name: Kirkpatrick - first_name: Carsten full_name: Sachse, Carsten last_name: Sachse - first_name: Hans full_name: Kraüsslich, Hans Georg last_name: Kraüsslich - first_name: John full_name: Briggs, John A last_name: Briggs citation: ama: Schur FK, Obr M, Hagen W, et al. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. Science. 2016;353(6298):506-508. doi:10.1126/science.aaf9620 apa: Schur, F. K., Obr, M., Hagen, W., Wan, W., Jakobi, A., Kirkpatrick, J., … Briggs, J. (2016). An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaf9620 chicago: Schur, Florian KM, Martin Obr, Wim Hagen, William Wan, Arjen Jakobi, Joanna Kirkpatrick, Carsten Sachse, Hans Kraüsslich, and John Briggs. “An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aaf9620. ieee: F. K. Schur et al., “An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation,” Science, vol. 353, no. 6298. American Association for the Advancement of Science, pp. 506–508, 2016. 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. Science. 353(6298), 506–508. mla: Schur, Florian KM, et al. “An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation.” Science, vol. 353, no. 6298, American Association for the Advancement of Science, 2016, pp. 506–08, doi:10.1126/science.aaf9620. short: F.K. Schur, M. Obr, W. Hagen, W. Wan, A. Jakobi, J. Kirkpatrick, C. Sachse, H. Kraüsslich, J. Briggs, Science 353 (2016) 506–508. date_created: 2018-12-11T11:48:39Z date_published: 2016-07-29T00:00:00Z date_updated: 2021-01-12T08:17:12Z day: '29' doi: 10.1126/science.aaf9620 extern: 1 intvolume: ' 353' issue: '6298' month: '07' page: 506 - 508 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '6834' quality_controlled: 0 status: public title: An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation type: journal_article volume: 353 year: '2016' ...