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- EMDB-0814: African swine fever virus major capsid protein p72 -

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Basic information

Entry
Database: EMDB / ID: EMD-0814
TitleAfrican swine fever virus major capsid protein p72
Map data
Sample
  • Virus: African swine fever virus
    • Protein or peptide: B646L,Major capsid protein
KeywordsAfrican Swine Fever virus capsomer / Trisymmetron / NCLDV / VIRAL PROTEIN
Function / homologyMajor capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / viral capsid / structural molecule activity / B646L
Function and homology information
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang N / Rao Z
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) releaseDec 4, 2019-
Map releaseMar 4, 2020-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l2t
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0814.png

Downloads & links

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Map

FileDownload / File: emd_0814.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 170 pix.
= 229.5 Å		1.35 Å/pix.
x 170 pix.
= 229.5 Å		1.35 Å/pix.
x 170 pix.
= 229.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 5
Minimum - Maximum-23.128962999999999 - 33.5854
Average (Standard dev.)0.037706587 (±1.1197252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170170
Spacing170170170
CellA=B=C: 229.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z170170170
origin x/y/z0.0000.0000.000
length x/y/z229.500229.500229.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS170170170
D min/max/mean-23.12933.5850.038

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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
    • Protein or peptide: B646L,Major capsid protein

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Supramolecule #1: African swine fever virus

SupramoleculeName: African swine fever virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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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Macromolecule #1: B646L,Major capsid protein

MacromoleculeName: B646L,Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 73.219562 KDa
SequenceString: MASGGAFCLI ANDGKADKII LAQDLLNSRI SNIKNVNKSY GKPDPEPTLS QIEETHLVHF NAHFKPYVPV GFEYNKVRPH TGTPTLGNK LTFGIPQYGD FFHDMVGHHI LGACHSSWQD APIQGTSQMG AHGQLQTFPR NGYDWDNQTP LEGAVYTLVD P FGRPIVPG ...String:
MASGGAFCLI ANDGKADKII LAQDLLNSRI SNIKNVNKSY GKPDPEPTLS QIEETHLVHF NAHFKPYVPV GFEYNKVRPH TGTPTLGNK LTFGIPQYGD FFHDMVGHHI LGACHSSWQD APIQGTSQMG AHGQLQTFPR NGYDWDNQTP LEGAVYTLVD P FGRPIVPG TKNAYRNLVY YCEYPGLRLY ENVRFEVNGN SLDEYSSDVT TLVRKFCIPG DKMTGYKHLV GQEVSVEGTS GP LLCNIHD LHKPHQSKPI LTDENDTQRT CSHTNPKFLS QHFPHFPENI QTAGKQDITP ITDATYLDIR RNVHYSCNGP QTP KYYQPP LALWIKLRFW FNDNVNLAIP SVSIPFGERF ITIKLASQKD LVNEFPGLFV RQSTVIAGRP SRRNIRFKPW FIPG VINEI SLTNNELYIN NLFVTPEIHN LYVKRVRFSL IRVHKTQVTH TNNNHHDEKL MSALKWPIEY MFIGLKPTWN ISDQN PHQH RDWHKFGHVV NAIMQPTHHA EISFQDRDTA LPDACSSISD ISPVTYPITL PIIKNISVTA HGINLIDKFP SQFCSS YIP FHYGGNAIKT PDDPGAMMIT FALYPREEYQ PSGHINVSRA REFYISWDSD YVGSITTADL VVSSSAINFL LLQNGSA VL RYST

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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

CTF correctionType: NONE
Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 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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