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

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Basic information

Entry
Database: PDB / ID: 6ku9
TitleStructure of the African swine fever virus major capsid protein p72
ComponentsB646L
KeywordsVIRAL PROTEIN / capsid 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsLiu, Q. / Xiang, Y.
Funding support China, 1items
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, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.2Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: B646L
B: B646L
C: B646L


Theoretical massNumber of molelcules
Total (without water)236,7923
Polymers236,7923
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, blue native PAGE
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein B646L / p72 / B646L CDS protein / Major capsid protein p72


Mass: 78930.531 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: p72, B646L, B646L CDS, ASFV-Georgia_4-106 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q5IZK2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: p72 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.73 MDa / Experimental value: NO
Source (natural)Organism: African swine fever virus
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293f
Details of virusIsolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: GraFix sample
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K / Details: blot 4.5s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 693388 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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