---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20935'
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.
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.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Ron
full_name: Kelley, Ron
last_name: Kelley
- first_name: Sagar
full_name: Khavnekar, Sagar
last_name: Khavnekar
- first_name: Ricardo D.
full_name: Righetto, Ricardo D.
last_name: Righetto
- first_name: Jessica
full_name: Heebner, Jessica
last_name: Heebner
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Xianjun
full_name: Zhang, Xianjun
last_name: Zhang
- first_name: Saikat
full_name: Chakraborty, Saikat
last_name: Chakraborty
- first_name: Grigory
full_name: Tagiltsev, Grigory
last_name: Tagiltsev
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Sofie
full_name: Van Dorst, Sofie
last_name: Van Dorst
- first_name: Florent
full_name: Waltz, Florent
last_name: Waltz
- first_name: Caitlyn L.
full_name: Mccafferty, Caitlyn L.
last_name: Mccafferty
- first_name: Lorenz
full_name: Lamm, Lorenz
last_name: Lamm
- first_name: Simon
full_name: Zufferey, Simon
last_name: Zufferey
- first_name: Philippe
full_name: Van Der Stappen, Philippe
last_name: Van Der Stappen
- first_name: Hugo
full_name: Van Den Hoek, Hugo
last_name: Van Den Hoek
- first_name: Wojciech
full_name: Wietrzynski, Wojciech
last_name: Wietrzynski
- first_name: Pavol
full_name: Harar, Pavol
id: e03d953a-6e8c-11ef-99e4-f0717d385cd5
last_name: Harar
orcid: 0000-0001-5206-1794
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: John A.G.
full_name: Briggs, John A.G.
last_name: Briggs
- first_name: Jürgen M.
full_name: Plitzko, Jürgen M.
last_name: Plitzko
- first_name: Benjamin D.
full_name: Engel, Benjamin D.
last_name: Engel
- first_name: Abhay
full_name: Kotecha, Abhay
last_name: Kotecha
citation:
ama: Kelley R, Khavnekar S, Righetto RD, et al. Toward community-driven visual proteomics
with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular
Cell. doi:10.1016/j.molcel.2025.11.029
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. Molecular Cell.
Elsevier. https://doi.org/10.1016/j.molcel.2025.11.029
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.”
Molecular Cell. Elsevier, n.d. https://doi.org/10.1016/j.molcel.2025.11.029.
ieee: R. Kelley et al., “Toward community-driven visual proteomics with large-scale
cryo-electron tomography of Chlamydomonas reinhardtii,” Molecular Cell.
Elsevier.
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.
mla: Kelley, Ron, et al. “Toward Community-Driven Visual Proteomics with Large-Scale
Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” Molecular Cell,
Elsevier, doi:10.1016/j.molcel.2025.11.029.
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.).
date_created: 2026-01-04T23:01:36Z
date_published: 2025-12-19T00:00:00Z
date_updated: 2026-01-05T08:32:47Z
day: '19'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.molcel.2025.11.029
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.molcel.2025.11.029
month: '12'
oa: 1
oa_version: Published Version
publication: Molecular Cell
publication_identifier:
eissn:
- 1097-4164
issn:
- 1097-2765
publication_status: inpress
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward community-driven visual proteomics with large-scale cryo-electron tomography
of Chlamydomonas reinhardtii
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
year: '2025'
...
---
APC_amount: 12348 EUR
OA_place: publisher
OA_type: hybrid
_id: '17884'
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.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
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.
article_processing_charge: Yes (in subscription journal)
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: Mathias
full_name: Percipalle, Mathias
id: 4986e21c-eb97-11eb-a6c2-a4ef0b629971
last_name: Percipalle
- first_name: Darya
full_name: Chernikova, Darya
id: 7dbaf460-fa9e-11eb-b0ca-bc7c7ff21ad0
last_name: Chernikova
- first_name: Huixin
full_name: Yang, Huixin
last_name: Yang
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Gergely
full_name: Pinke, Gergely
id: 4D5303E6-F248-11E8-B48F-1D18A9856A87
last_name: Pinke
- first_name: Dario J
full_name: Porley, Dario J
id: 2FD6EA6C-F248-11E8-B48F-1D18A9856A87
last_name: Porley
- first_name: Louis M.
full_name: Mansky, Louis M.
last_name: Mansky
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
- 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, Percipalle M, Chernikova D, et al. Distinct stabilization of the human
T cell leukemia virus type 1 immature Gag lattice. Nature Structural &
Molecular Biology. 2025;32:268-276. doi:10.1038/s41594-024-01390-8
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. Nature Structural & Molecular Biology.
Springer Nature. https://doi.org/10.1038/s41594-024-01390-8
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.” Nature Structural & Molecular Biology.
Springer Nature, 2025. https://doi.org/10.1038/s41594-024-01390-8.
ieee: M. Obr et al., “Distinct stabilization of the human T cell leukemia
virus type 1 immature Gag lattice,” Nature Structural & Molecular Biology,
vol. 32. Springer Nature, pp. 268–276, 2025.
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 & Molecular
Biology. 32, 268–276.
mla: Obr, Martin, et al. “Distinct Stabilization of the Human T Cell Leukemia Virus
Type 1 Immature Gag Lattice.” Nature Structural & Molecular Biology,
vol. 32, Springer Nature, 2025, pp. 268–76, doi:10.1038/s41594-024-01390-8.
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 & Molecular
Biology 32 (2025) 268–276.
corr_author: '1'
date_created: 2024-09-08T10:29:06Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2026-03-16T12:55:18Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
- _id: LeSa
doi: 10.1038/s41594-024-01390-8
external_id:
isi:
- '001306564000001'
oaworkid:
- W4402316284
pmid:
- '39242978'
file:
- access_level: open_access
checksum: c641ad94afb28917b20425db676fc3ee
content_type: application/pdf
creator: dernst
date_created: 2025-04-23T07:02:33Z
date_updated: 2025-04-23T07:02:33Z
file_id: '19608'
file_name: 2025_NatureStrucBio_Obr.pdf
file_size: 13724041
relation: main_file
success: 1
file_date_updated: 2025-04-23T07:02:33Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
oaworkid: 1
page: 268-276
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
- _id: 9B9C98E0-BA93-11EA-9121-9846C619BF3A
grant_number: '25762'
name: Structural characterization of spumavirus capsid assemblies to understand
conserved Ortervirales assembly mechanisms
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct stabilization of the human T cell leukemia virus type 1 immature Gag
lattice
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: 32
year: '2025'
...
---
_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: 2025-04-15T08:24:50Z
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
orcid: 0000-0003-1756-6564
- 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: 2025-04-15T08:24:49Z
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
orcid: 0000-0003-1756-6564
- 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).
corr_author: '1'
date_created: 2022-04-15T07:10:26Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2025-04-15T08:24:50Z
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
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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: '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).
corr_author: '1'
date_created: 2021-10-07T09:13:29Z
date_published: 2021-09-17T00:00:00Z
date_updated: 2025-04-15T08:24:49Z
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'
scopus_import: '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: '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
orcid: 0000-0003-1756-6564
- 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).
corr_author: '1'
date_created: 2021-05-28T14:25:50Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2025-04-15T08:24:49Z
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: '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: 2026-04-03T09:27:26Z
day: '13'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1038/s41467-020-14535-2
external_id:
isi:
- '000514928000017'
pmid:
- '32054835'
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
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
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.
article_processing_charge: No
author:
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Wim
full_name: Hagen, Wim
last_name: Hagen
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: Arjen
full_name: Jakobi, Arjen
last_name: Jakobi
- first_name: Joanna
full_name: Kirkpatrick, Joanna
last_name: Kirkpatrick
- first_name: Carsten
full_name: Sachse, Carsten
last_name: Sachse
- first_name: Hans
full_name: Kraüsslich, Hans
last_name: Kraüsslich
- first_name: John
full_name: Briggs, John
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. Vol 353. American Association
for the Advancement of Science; 2016:506-508. 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 (Vol. 353, pp. 506–508). 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.
Vol. 353. 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, vol. 353. American Association
for the Advancement of Science, 2016, pp. 506–508.
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.
mla: Schur, Florian KM, et al. An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures
Regulating Assembly and Maturation. Vol. 353, 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, An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures
Regulating Assembly and Maturation, American Association for the Advancement of
Science, 2016.
date_created: 2018-12-11T11:48:39Z
date_published: 2016-07-29T00:00:00Z
date_updated: 2026-05-20T07:41:16Z
day: '29'
doi: 10.1126/science.aaf9620
extern: '1'
external_id:
pmid:
- '27417497'
intvolume: ' 353'
language:
- iso: eng
month: '07'
oa_version: None
page: 506 - 508
pmid: 1
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6834'
scopus_import: '1'
status: public
title: An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly
and maturation
type: report
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 353
year: '2016'
...