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- EMDB-0776: Structure of the African swine fever virus major capsid protein p72 -

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Basic information

Entry
Database: EMDB / ID: EMD-0776
TitleStructure of the African swine fever virus major capsid protein p72
Map datasharpened map
Sample
  • Complex: p72
    • Protein or peptide: B646L
Keywordscapsid protein / 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: 2.67 Å
AuthorsLiu Q / Xiang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Cell Res / Year: 2019
Title: Structure of the African swine fever virus major capsid protein p72.
Authors: Qi Liu / Bingting Ma / Nianchao Qian / Fan Zhang / Xu Tan / Jianlin Lei / Ye Xiang /
History
DepositionAug 31, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.036
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ku9
  • Surface level: 0.036
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0776.png

Downloads & links

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Map

FileDownload / File: emd_0776.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 261.84 Å		1.09 Å/pix.
x 240 pix.
= 261.84 Å		1.09 Å/pix.
x 240 pix.
= 261.84 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.036 / Movie #1: 0.036
Minimum - Maximum-0.1619708 - 0.30497512
Average (Standard dev.)0.00018688843 (±0.0061823456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 261.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z261.840261.840261.840
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/NS240240240
D min/max/mean-0.1620.3050.000

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Supplemental data

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Mask #1

Fileemd_0776_msk_1.map
Projections & Slices
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Additional map: unsharpened map

Fileemd_0776_additional.map
Annotationunsharpened map
Projections & Slices
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Histogram

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Additional map: unsharpened map

Fileemd_0776_additional_1.map
Annotationunsharpened map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map

Fileemd_0776_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_0776_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : p72

EntireName: p72
Components
  • Complex: p72
    • Protein or peptide: B646L

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Supramolecule #1: p72

SupramoleculeName: p72 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 730 KDa

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Macromolecule #1: B646L

MacromoleculeName: B646L / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 78.930531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHH HGSDYKDHDG DYKDHDIDYK DDDDKELENL YFQGAGSMAS GGAFCLIAND GKADKIILAQ DLLNSRISNI KNVNKSYGK PDPEPTLSQI EETHLVHFNA HFKPYVPVGF EYNKVRPHTG TPTLGNKLTF GIPQYGDFFH DMVGHHILGA C HSSWQDAP ...String:
MHHHHHHHHH HGSDYKDHDG DYKDHDIDYK DDDDKELENL YFQGAGSMAS GGAFCLIAND GKADKIILAQ DLLNSRISNI KNVNKSYGK PDPEPTLSQI EETHLVHFNA HFKPYVPVGF EYNKVRPHTG TPTLGNKLTF GIPQYGDFFH DMVGHHILGA C HSSWQDAP IQGTSQMGAH GQLQTFPRNG YDWDNQTPLE GAVYTLVDPF GRPIVPGTKN AYRNLVYYCE YPGERLYENV RF DVNGNSL DEYSSDVTTL VRKFCIPGDK MTGYKHLVGQ EVSVEGTSGP LLCNIHDLHK PHQSKPILTD ENDTQRTCSH TNP KFLSQH FPENSHNIQT AGKQDITPIT DATYLDIRRN VHYSCNGPQT PKYYQPPLAL WIKLRFWFNE NVNLAIPSVS IPFG ERFIT IKLASQKDLV NEFPGLFVRQ SRFIAGRPSR RNIRFKPWFI PGVINEISLT NNELYINNLF VTPEIHNLFV KRVRF SLIR VHKTQVTHTN NNHHDEKLMS ALKWPIEYMF IGLKPTWNIS DQNPHQHRDW HKFGHVVNAI MQPTHHAEIS FQDRDT ALP DACSSISDIS PVTYPITLPI IKNISVTAHG INLIDKFPSK FCSSYIPFHY GGNAIKTPDD PGAMMITFAL KPREEYQ PS GHINVSRARE FYISWDTDYV GSITTADLVV SASAINFLLL QNGSAVLRYS T

UniProtKB: B646L

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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

Concentration0.4 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot 4.5s.
DetailsGraFix sample

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 693388
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6ku9:
Structure of the African swine fever virus major capsid protein p72

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