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- EMDB-0815: African Swine Fever Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-0815
TitleAfrican Swine Fever Virus
Map dataAfrican Swine Fever Viron
Sample
  • Virus: African swine fever virus
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsWang X / Wang N
CitationJournal: Science / Year: 2019
Title: Architecture of African swine fever virus and implications for viral assembly.
Authors: Nan Wang / Dongming Zhao / Jialing Wang / Yangling Zhang / Ming Wang / Yan Gao / Fang Li / Jingfei Wang / Zhigao Bu / Zihe Rao / Xiangxi Wang /
Abstract: African swine fever virus (ASFV) is a giant and complex DNA virus that causes a highly contagious and often lethal swine disease for which no vaccine is available. Using an optimized image ...African swine fever virus (ASFV) is a giant and complex DNA virus that causes a highly contagious and often lethal swine disease for which no vaccine is available. Using an optimized image reconstruction strategy, we solved the ASFV capsid structure up to 4.1 angstroms, which is built from 17,280 proteins, including one major (p72) and four minor (M1249L, p17, p49, and H240R) capsid proteins organized into pentasymmetrons and trisymmetrons. The atomic structure of the p72 protein informs putative conformational epitopes, distinguishing ASFV from other nucleocytoplasmic large DNA viruses. The minor capsid proteins form a complicated network below the outer capsid shell, stabilizing the capsid by holding adjacent capsomers together. Acting as core organizers, 100-nanometer-long M1249L proteins run along each edge of the trisymmetrons that bridge two neighboring pentasymmetrons and form extensive intermolecular networks with other capsid proteins, driving the formation of the capsid framework. These structural details unveil the basis of capsid stability and assembly, opening up new avenues for African swine fever vaccine development.
History
DepositionOct 6, 2019-
Header (metadata) releaseNov 20, 2019-
Map releaseNov 20, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0815.png

Downloads & links

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Map

FileDownload / File: emd_0815.map.gz / Format: CCP4 / Size: 5.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAfrican Swine Fever Viron
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.68 Å/pix.
x 1150 pix.
= 3082. Å		2.68 Å/pix.
x 1150 pix.
= 3082. Å		2.68 Å/pix.
x 1150 pix.
= 3082. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.3 / Movie #1: 2.3
Minimum - Maximum-9.606571 - 12.206113
Average (Standard dev.)0.073820256 (±0.8826007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions115011501150
Spacing115011501150
CellA=B=C: 3082.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.682.682.68
M x/y/z115011501150
origin x/y/z0.0000.0000.000
length x/y/z3082.0003082.0003082.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS115011501150
D min/max/mean-9.60712.2060.074

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Supplemental data

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Sample components

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Entire : African swine fever virus

EntireName: African swine fever virus
Components
  • Virus: African swine fever virus

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Supramolecule #1: African swine fever virus

SupramoleculeName: African swine fever virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10497 / Sci species name: African swine fever virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
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: 35.0 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 reconstructionResolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43811
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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