› 6ki3

X-ray diffraction
2.35Å resolution

The crystal structure of AsfvAP:dF commplex

Released:
DOI: 10.2210/pdb6ki3/pdb
PDB entry 6ki3 coloured by chain, front view.
PDB entry 6ki3 coloured by chain, side view.
PDB entry 6ki3 coloured by chain, top view.
Source organisms:
Primary publication:
A unique DNA-binding mode of African swine fever virus AP endonuclease.
Chen Y, Chen X, Huang Q, Shao Z, Gao Y, Li Y, Yang C, Liu H, Li J, Wang Q, Ma J, Zhang YZ, Gu Y, Gan J
Cell Discov 6 13 (2020)
PMID: 32194979

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120151 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Probable AP endonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 301 amino acids
Theoretical weight: 33.84 KDa
Source organism: African swine fever virus tick/South Africa/Pretoriuskop Pr4/1996
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0C9C6 (Residues: 1-296; Coverage: 100%)
Gene name: Pret-146
Sequence domains: Xylose isomerase-like TIM barrel
DNA (5'-D(*GP*CP*AP*GP*CP*GP*TP*CP*C)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 9 nucleotides
Theoretical weight: 2.72 KDa
Source organism: African swine fever virus
Expression system: Not provided
DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*AP*G)-3') Chains: D, G
Molecule details ›
Chains: D, G
Length: 8 nucleotides
Theoretical weight: 2.33 KDa
Source organism: African swine fever virus
Expression system: Not provided
DNA (5'-D(*CP*CP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*CP*TP*G)-3') Chains: E, H
Molecule details ›
Chains: E, H
Length: 17 nucleotides
Theoretical weight: 5.22 KDa
Source organism: African swine fever virus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P21
Unit cell:
a: 50.637Å b: 84.698Å c: 98.585Å
α: 90° β: 93.66° γ: 90°
R-values:
R R work R free
0.209 0.208 0.244
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

10 citation in other articles

Deletion of the A137R Gene from the Pandemic Strain of African Swine Fever Virus Attenuates the Strain and Offers Protection against the Virulent Pandemic Virus.
Gladue et al. (2021)
9 more

2 mentions without citation

Structures and Functional Diversities of ASFV Proteins.
Wang et al. (2021)
1 more