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- PDB-8y3q: ASFV p72 in complex with Fab F11 -

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Basic information

Entry
Database: PDB / ID: 8y3q
TitleASFV p72 in complex with Fab F11
Components
  • B646L
  • Heavy chain of F11
  • Light chain of F11
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / ASFV / P72 / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsWang, X. / Fu, W. / Yu, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Discov / Year: 2024
Title: p72 antigenic mapping reveals a potential supersite of vulnerability for African swine fever virus.
Authors: Qi Yu / Dening Liang / Wangjun Fu / Li Zhang / Jinglin Wang / Zhenjiang Zhang / Yao Sun / Dandan Zhu / BinYang Zheng / Ling Zhu / Ye Xiang / Dongming Zhao / Xiangxi Wang /
History
DepositionJan 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B646L
D: Heavy chain of F11
E: Heavy chain of F11
F: Heavy chain of F11
G: Light chain of F11
H: Light chain of F11
I: Light chain of F11
B: B646L
C: B646L


Theoretical massNumber of molelcules
Total (without water)310,3539
Polymers310,3539
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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 / Production host: Homo sapiens (human) / References: UniProt: Q5IZK2
#2: Antibody Heavy chain of F11


Mass: 13016.646 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig)
#3: Antibody Light chain of F11


Mass: 11503.765 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig)
Has protein modificationY

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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: ASFV p72 in complex with Fab F11 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11African swine fever virus10497
21Sus scrofa (pig)9823
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Sus scrofa (pig)9823
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 531306 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316182
ELECTRON MICROSCOPYf_angle_d0.51822032
ELECTRON MICROSCOPYf_dihedral_angle_d4.3822175
ELECTRON MICROSCOPYf_chiral_restr0.0452376
ELECTRON MICROSCOPYf_plane_restr0.0052859

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