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- EMDB-15268: Tomogram of an Ebola VLP composed of VP40 at pH 4.5 (Figure 1J) -

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Basic information

Entry
Database: EMDB / ID: EMD-15268
TitleTomogram of an Ebola VLP composed of VP40 at pH 4.5 (Figure 1J)
Map data
Sample
  • Virus: Ebola virus - Mayinga, Zaire, 1976
KeywordsEbola VLP / VP40 matrix / low pH / VIRUS LIKE PARTICLE / cryo-ET
Biological speciesEbola virus - Mayinga, Zaire, 1976
Methodelectron tomography / cryo EM
AuthorsWinter SL / Chlanda P
Funding support1 items
OrganizationGrant numberCountry
Other privateChica and Heinz Schaller Foundation
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
DepositionJun 27, 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_15268.png

Downloads & links

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Map

FileDownload / File: emd_15268.map.gz / Format: CCP4 / Size: 172.6 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 8.013 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)1.5954589 (±12.069929999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions1364560237
Spacing5601364237
CellA: 4487.28 Å / B: 10929.731 Å / C: 1899.0809 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: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes

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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: 4.5
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

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

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41

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