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- EMDB-15956: Tomogram of an extracellular EBOV particle adjacent to an EBOV-in... -

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Basic information

Entry
Database: EMDB / ID: EMD-15956
TitleTomogram of an extracellular EBOV particle adjacent to an EBOV-infected Huh7 cell
Map dataTomogram of an extracellular EBOV particle adjacent to an EBOV-infected Huh7 cell
Sample
  • Virus: Ebola virus - Mayinga, Zaire, 1976
KeywordsEbola virus / neutral pH / VIRUS
Biological speciesEbola virus - Mayinga, Zaire, 1976
Methodelectron tomography / cryo EM
AuthorsWinter SL / Chlanda P
Funding support Germany, 1 items
OrganizationGrant numberCountry
Other privateChica and Heinze Schaller Foundation Germany
CitationJournal: EMBO J / Year: 2023
Title: The Ebola virus VP40 matrix layer undergoes endosomal disassembly essential for membrane fusion.
Authors: Sophie L Winter / Gonen Golani / Fabio Lolicato / Melina Vallbracht / Keerthihan Thiyagarajah / Samy Sid Ahmed / Christian Lüchtenborg / Oliver T Fackler / Britta Brügger / Thomas Hoenen / ...Authors: Sophie L Winter / Gonen Golani / Fabio Lolicato / Melina Vallbracht / Keerthihan Thiyagarajah / Samy Sid Ahmed / Christian Lüchtenborg / Oliver T Fackler / Britta Brügger / Thomas Hoenen / Walter Nickel / Ulrich S Schwarz / Petr Chlanda /
Abstract: Ebola viruses (EBOVs) assemble into filamentous virions, whose shape and stability are determined by the matrix viral protein 40 (VP40). Virus entry into host cells occurs via membrane fusion in late ...Ebola viruses (EBOVs) assemble into filamentous virions, whose shape and stability are determined by the matrix viral protein 40 (VP40). Virus entry into host cells occurs via membrane fusion in late endosomes; however, the mechanism of how the remarkably long virions undergo uncoating, including virion disassembly and nucleocapsid release into the cytosol, remains unknown. Here, we investigate the structural architecture of EBOVs entering host cells and discover that the VP40 matrix disassembles prior to membrane fusion. We reveal that VP40 disassembly is caused by the weakening of VP40-lipid interactions driven by low endosomal pH that equilibrates passively across the viral envelope without a dedicated ion channel. We further show that viral membrane fusion depends on VP40 matrix integrity, and its disassembly reduces the energy barrier for fusion stalk formation. Thus, pH-driven structural remodeling of the VP40 matrix acts as a molecular switch coupling viral matrix uncoating to membrane fusion during EBOV entry.
History
DepositionOct 13, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15956.png

Downloads & links

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Map

FileDownload / File: emd_15956.map.gz / Format: CCP4 / Size: 507 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomogram of an extracellular EBOV particle adjacent to an EBOV-infected Huh7 cell
Voxel sizeX=Y=Z: 8.013 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)25.845991000000001 (±13.357084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-834834-321
Dimensions19201364203
Spacing13641920203
CellA: 10929.731 Å / B: 15384.959 Å / C: 1626.6389 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ebola virus - Mayinga, Zaire, 1976

EntireName: Ebola virus - Mayinga, Zaire, 1976
Components
  • Virus: Ebola virus - Mayinga, Zaire, 1976

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Supramolecule #1: Ebola virus - Mayinga, Zaire, 1976

SupramoleculeName: Ebola virus - Mayinga, Zaire, 1976 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 128952 / Sci species name: Ebola virus - Mayinga, Zaire, 1976 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.3 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 6000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos FIB-SEM. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 33000
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 41

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