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- EMDB-11665: Structure of GP in EBOV VP40-GP VLPs -

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Basic information

Entry
Database: EMDB / ID: EMD-11665
TitleStructure of GP in EBOV VP40-GP VLPs
Map dataStructure of GP in EBOV VP40-GP VLPs
Sample
  • Virus: Ebola virus - Mayinga, Zaire, 1976
    • Protein or peptide: GP
Biological speciesEbola virus - Mayinga / Ebola virus - Mayinga, Zaire, 1976
Methodsubtomogram averaging / cryo EM / Resolution: 12.8 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: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11665.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of GP in EBOV VP40-GP VLPs
Voxel sizeX=Y=Z: 1.78 Å
Density
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.15781736 - 0.291098
Average (Standard dev.)0.0020586983 (±0.050520673)
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-0.1580.2910.002

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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: GP

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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: GP

MacromoleculeName: GP / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Mayinga
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGVTGILQLP RDRFKRTSFF LWVIILFQRT FSIPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLN LEGNGVATDV PSATKRWGFR SGVPPKVVNY EAGEWAENCY NLEIKKPDGS E CLPAAPDG IRGFPRCRYV HKVSGTGPCA GDFAFHKEGA FFLYDRLAST ...String:
MGVTGILQLP RDRFKRTSFF LWVIILFQRT FSIPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLN LEGNGVATDV PSATKRWGFR SGVPPKVVNY EAGEWAENCY NLEIKKPDGS E CLPAAPDG IRGFPRCRYV HKVSGTGPCA GDFAFHKEGA FFLYDRLAST VIYRGTTFAE GV VAFLILP QAKKDFFSSH PLREPVNATE DPSSGYYSTT IRYQATGFGT NETEYLFEVD NLT YVQLES RFTPQFLLQL NETIYTSGKR SNTTGKLIWK VNPEIDTTIG EWAFWETKKN LTRK IRSEE LSFTVVSNGA KNISGQSPAR TSSDPGTNTT TEDHKIMASE NSSAMVQVHS QGREA AVSH LTTLATISTS PQSLTTKPGP DNSTHNTPVY KLDISEATQV EQHHRRTDND STASDT PSA TTAAGPPKAE NTNTSKSTDF LDPATTTSPQ NHSETAGNNN THHQDTGEES ASSGKLG LI TNTIAGVAGL ITGGRRTRRE AIVNAQPKCN PNLHYWTTQD EGAAIGLAWI PYFGPAAE G IYIEGLMHNQ DGLICGLRQL ANETTQALQL FLRATTELRT FSILNRKAID FLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDKTLPDQGD NDNWWTGWRQ WIPAGIGVTG VIIAVIALF CICKFVF

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

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Image processing

ExtractionNumber tomograms: 55 / Number images used: 164205
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4)defocus determination
CTFPHASEFLIPCTF correction
Final angle assignmentType: OTHER / Software: (Name: TOM, AV3) / Details: Constrained Cross Correlation
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 12.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: AV3 / Number subtomograms used: 11188

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