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- EMDB-0845: Cryo-EM structure of African Swine Fever Virus capsid block 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-0845
TitleCryo-EM structure of African Swine Fever Virus capsid block 2
Map data
SampleAfrican swine fever virus:
virus
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.62 Å
AuthorsGao GF / Liu S
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesKJZD-SW-L06-01 China
CitationJournal: Cell Host Microbe / Year: 2019
Title: Cryo-EM Structure of the African Swine Fever Virus.
Authors: Sheng Liu / Yuzi Luo / Yajuan Wang / Shihua Li / Zhennan Zhao / Yuhai Bi / Junqing Sun / Ruchao Peng / Hao Song / Dongjie Zhu / Yuan Sun / Su Li / Li Zhang / Wei Wang / Yeping Sun / Jianxun Qi / Jinghua Yan / Yi Shi / Xinzheng Zhang / Peiyi Wang / Hua-Ji Qiu / George F Gao /
Abstract: African swine fever virus (ASFV) is a large double-stranded DNA virus with an icosahedral multilayered structure. ASFV causes a lethal swine hemorrhagic disease and is currently responsible for ...African swine fever virus (ASFV) is a large double-stranded DNA virus with an icosahedral multilayered structure. ASFV causes a lethal swine hemorrhagic disease and is currently responsible for widespread damage to the pork industry in Asia. Neither vaccines nor antivirals are available and the molecular characterization of the ASFV particle is outstanding. Here, we describe the cryogenic electron microscopy (cryo-EM) structure of the icosahedral capsid of ASFV at 4.6-Å. The ASFV particle consists of 8,280 copies of the major capsid protein p72, 60 copies of the penton protein, and at least 8,340 minor capsid proteins, of which there might be 3 different types. Like other nucleocytoplasmic large DNA viruses, the minor capsid proteins form a hexagonal network below the outer capsid shell, functioning as stabilizers by "gluing" neighboring capsomers together. Our findings provide a comprehensive molecular model of the ASFV capsid architecture that will contribute to the future development of countermeasures, including vaccines.
History
DepositionNov 1, 2019-
Header (metadata) releaseDec 11, 2019-
Map releaseDec 11, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.004
  • 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_0845.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 400 pix.
= 564. Å
1.41 Å/pix.
x 400 pix.
= 564. Å
1.41 Å/pix.
x 400 pix.
= 564. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.41 Å
Density
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.019235399 - 0.027822763
Average (Standard dev.)0.00008627639 (±0.0012992079)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 564.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.411.411.41
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z564.000564.000564.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0190.0280.000

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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 / Number of components: 1

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Component #1: virus, African swine fever virus

VirusName: African swine fever virus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: African swine fever virus

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / 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: 1.25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 180000
3D reconstructionResolution: 4.62 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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