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- EMDB-0846: Cryo-EM structure of African Swine Fever Virus capsid block 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-0846
TitleCryo-EM structure of African Swine Fever Virus capsid block 1
Map dataCryo-EM structure of African Swine Fever Virus capsid block 1
Sample
  • Virus: African swine fever virus
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.66 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 ...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 9, 2020-
Current statusDec 9, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0846.png

Downloads & links

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Map

FileDownload / File: emd_0846.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of African Swine Fever Virus capsid block 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 440 pix.
= 620.4 Å		1.41 Å/pix.
x 440 pix.
= 620.4 Å		1.41 Å/pix.
x 440 pix.
= 620.4 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.018937394 - 0.027110819
Average (Standard dev.)0.000051586 (±0.0009648768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 620.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.411.411.41
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z620.400620.400620.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0190.0270.000

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Supplemental data

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Additional map: Cryo-EM structure of African Swine Fever Virus capsid asymmetric unit

Fileemd_0846_additional.map
AnnotationCryo-EM structure of African Swine Fever Virus capsid asymmetric unit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryo-EM structure of African Swine Fever Virus capsid asymmetric unit

Fileemd_0846_additional_1.map
AnnotationCryo-EM structure of African Swine Fever Virus capsid asymmetric unit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: STRAIN / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.25 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: 4.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 164280
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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