[English] 日本語
Yorodumi
- EMDB-11662: Structure of VP40 matrix layer in EBOV VP40-GP VLPs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11662
TitleStructure of VP40 matrix layer in EBOV VP40-GP VLPs
Map dataStructure of VP40 matrix layer in EBOV VP40-GP 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: 9.9 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11662.png

Downloads & links

-
Map

FileDownload / File: emd_11662.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of VP40 matrix layer in EBOV VP40-GP 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: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.1891876 - 0.21138175
Average (Standard dev.)0.0010036809 (±0.06802714)
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-0.1890.2110.001

-
Supplemental data

-
Sample components

-
Entire : Ebola virus - Mayinga, Zaire, 1976

EntireName: Ebola virus - Mayinga, Zaire, 1976
Components
  • Virus: Ebola virus - Mayinga, Zaire, 1976
    • Protein or peptide: VP40

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: AV3 / Number subtomograms used: 106793
ExtractionNumber tomograms: 55 / Number images used: 106793
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4)defocus determination
CTFPHASEFLIPCTF correction
Final angle assignmentType: OTHER / Software: (Name: TOM, AV3) / Details: Constrained Cross Correlation

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more