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- PDB-9m72: ASFV p15 in complex with Fab 4E2 -

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Basic information

Entry
Database: PDB / ID: 9m72
TitleASFV p15 in complex with Fab 4E2
Components
  • Heavy chain of 4E2
  • Light chain of 4E2
  • p15
KeywordsVIRAL PROTEIN / ASFV / p15 / antibody
Function / homologyviral capsid assembly / virion component / host cell perinuclear region of cytoplasm / Polyprotein pp62
Function and homology information
Biological speciesAfrican swine fever virus
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsWang, X. / Yu, Q. / Fu, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: ASFV p15 in complex with Fab 4E2
Authors: Wang, X. / Yu, Q. / Fu, W.
History
DepositionMar 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: p15
A: Heavy chain of 4E2
B: Light chain of 4E2
H: p15
D: Heavy chain of 4E2
F: Light chain of 4E2
I: p15
E: Heavy chain of 4E2
G: Light chain of 4E2


Theoretical massNumber of molelcules
Total (without water)125,2839
Polymers125,2839
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 p15


Mass: 16842.590 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus (strain Badajoz 1971 Vero-adapted)
Gene: Ba71V-94, CP530R / Production host: Escherichia coli (E. coli) / References: UniProt: Q65179
#2: Antibody Heavy chain of 4E2


Mass: 12983.256 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Mus musculus (house mouse)
#3: Antibody Light chain of 4E2


Mass: 11935.083 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Mus musculus (house mouse)
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 p15 in complex with Fab 4E2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Sus scrofa (pig)9823
21African swine fever virus (strain Badajoz 1971 Vero-adapted)10498
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Escherichia coli (E. coli)562
21Mus musculus (house mouse)10090
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: TFS 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 / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266941 / Symmetry type: POINT
RefinementHighest resolution: 3.75 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029006
ELECTRON MICROSCOPYf_angle_d0.42912204
ELECTRON MICROSCOPYf_dihedral_angle_d3.6251215
ELECTRON MICROSCOPYf_chiral_restr0.041335
ELECTRON MICROSCOPYf_plane_restr0.0031557

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