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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 dataStructure of VP40 matrix layer in EBOV VP40 VLPs
Sample
  • Virus: Ebola virus - Mayinga, Zaire, 1976
    • Protein or peptide: VP40
Biological speciesEbola virus - Mayinga / Ebola virus - Mayinga, Zaire, 1976
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 Ollmann 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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11661.png

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)
AnnotationStructure of VP40 matrix layer in EBOV VP40 VLPs
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

Histogram

Histogram (log scale)
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
Components
  • Virus: Ebola virus - Mayinga, Zaire, 1976
    • Protein or peptide: VP40

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

SupramoleculeName: Ebola virus - Mayinga, Zaire, 1976 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 128952 / Sci species name: Ebola virus - Mayinga, Zaire, 1976 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes
Host systemOrganism: Homo sapiens (human)

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Macromolecule #1: VP40

MacromoleculeName: VP40 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Mayinga
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRRVILPTAP PEYMEAIYPV RSNSTIARGG NSNTGFLTPE SVNGDTPSNP LRPIADDTID HASHTPGSV SSAFILEAMV NVISGPKVLM KQIPIWLPLG VADQKTYSFD STTAAIMLAS Y TITHFGKA TNPLVRVNRL GPGIPDHPLR LLRIGNQAFL QEFVLPPVQL ...String:
MRRVILPTAP PEYMEAIYPV RSNSTIARGG NSNTGFLTPE SVNGDTPSNP LRPIADDTID HASHTPGSV SSAFILEAMV NVISGPKVLM KQIPIWLPLG VADQKTYSFD STTAAIMLAS Y TITHFGKA TNPLVRVNRL GPGIPDHPLR LLRIGNQAFL QEFVLPPVQL PQYFTFDLTA LK LITQPLP AATWTDDTPT GSNGALRPGI SFHPKLRPIL LPNKSGKKGN SADLTSPEKI QAI MTSLQD FKIVPIDPTK NIMGIEVPET LVHKLTGKKV TSKNGQPIIP VLLPKYIGLD PVAP GDLTM VITQDCDTCH SPASLPAVIE K

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: AV3 / Number subtomograms used: 20352
ExtractionNumber tomograms: 39 / Number images used: 480095
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4)defocus determination
CTFPHASEFLIPCTF correction
Final angle assignmentType: OTHER / Software: (Name: TOM, AV3) / Details: Constrained Cross Correlation

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