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- EMDB-11661: Structure of VP40 matrix layer in EBOV VP40 VLPs -

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Basic information

Entry
Database: EMDB / ID: EMD-11661
TitleStructure of VP40 matrix layer in EBOV VP40 VLPs
Map data
SampleEbola virus - Mayinga, Zaire, 1976:
virus / VP40
Biological speciesEbola virus - Mayinga, Zaire, 1976 / Ebola virus - Mayinga
Methodsubtomogram averaging / cryo EM / Resolution: 9.8 Å
AuthorsWan W / Clarke M / Norris M / Kolesnikova L / Koehler A / Bornholdt ZA / Becker S / Saphire EO / Briggs JAG
Funding supportEuropean Union, Germany, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-648432 MEMBRANEFUSIONEuropean Union
European Molecular Biology Organization (EMBO)ALTF 748-2014European Union
German Research Foundation (DFG)Sonderforschungsbereich 1021 Germany
CitationJournal: Elife / Year: 2020
Title: Ebola and Marburg virus matrix layers are locally ordered assemblies of VP40 dimers.
Authors: William Wan / Mairi Clarke / Michael J Norris / Larissa Kolesnikova / Alexander Koehler / Zachary A Bornholdt / Stephan Becker / Erica Ollman-Saphire / John Ag Briggs /
Abstract: Filoviruses such as Ebola and Marburg virus bud from the host membrane as enveloped virions. This process is achieved by the matrix protein VP40. When expressed alone, VP40 induces budding of ...Filoviruses such as Ebola and Marburg virus bud from the host membrane as enveloped virions. This process is achieved by the matrix protein VP40. When expressed alone, VP40 induces budding of filamentous virus-like particles, suggesting that localization to the plasma membrane, oligomerization into a matrix layer, and generation of membrane curvature are intrinsic properties of VP40. There has been no direct information on the structure of VP40 matrix layers within viruses or virus-like particles. We present structures of Ebola and Marburg VP40 matrix layers in intact virus-like particles, and within intact Marburg viruses. VP40 dimers assemble extended chains via C-terminal domain interactions. These chains stack to form 2D matrix lattices below the membrane surface. These lattices form a patchwork assembly across the membrane and suggesting that assembly may begin at multiple points. Our observations define the structure and arrangement of the matrix protein layer that mediates formation of filovirus particles.
History
DepositionAug 24, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11661.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 192 pix.
= 341.76 Å
1.78 Å/pix.
x 192 pix.
= 341.76 Å
1.78 Å/pix.
x 192 pix.
= 341.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density
Contour LevelBy AUTHOR: 0.35 / Movie #1: 0.35
Minimum - Maximum-1.9970478 - 1.8306116
Average (Standard dev.)0.001210799 (±0.34741125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 341.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z341.760341.760341.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ161186271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-1.9971.8310.001

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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 / Number of components: 2

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

VirusName: Ebola virus - Mayinga, Zaire, 1976 / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: Yes / Isolate: SPECIES
SpeciesSpecies: Ebola virus - Mayinga, Zaire, 1976
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, VP40

ProteinName: VP40 / Recombinant expression: No
SourceSpecies: Ebola virus - Mayinga
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C2 (2 fold cyclic) / Number of subtomograms: 20352
3D reconstructionSoftware: AV3 / Resolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Constrained Cross Correlation

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