› 7v7c

Electron Microscopy
3.7Å resolution

CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex

Released:
DOI: 10.2210/pdb7v7c/pdb
PDB entry 7v7c coloured by chain, front view.
PDB entry 7v7c coloured by chain, side view.
PDB entry 7v7c coloured by chain, top view.
Source organisms:
Entry authors: Wang D, Xu J, Liu Q, Xiang Y
Related structures: EMD-31766

Function and Biology Details

Reactions catalysed: 
ATP + a protein = ADP + a phosphoprotein
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-146253 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
DDB1- and CUL4-associated factor 1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 1507 amino acids
Theoretical weight: 169.19 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9Y4B6 (Residues: 1-1507; Coverage: 100%)
Gene names: DCAF1, KIAA0800, RIP, VPRBP
DNA damage-binding protein 1 Chains: B, F
Molecule details ›
Chains: B, F
Length: 1140 amino acids
Theoretical weight: 127.1 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 100%)
Gene names: DDB1, XAP1
Sequence domains:
Protein Vpr Chains: C, G
Molecule details ›
Chains: C, G
Length: 96 amino acids
Theoretical weight: 11.4 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P12520 (Residues: 1-96; Coverage: 100%)
Gene name: vpr
Sequence domains: VPR/VPX protein
Uracil-DNA glycosylase Chains: D, H
Molecule details ›
Chains: D, H
Length: 220 amino acids
Theoretical weight: 25.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P13051 (Residues: 94-313; Coverage: 70%)
Gene names: DGU, UNG, UNG1, UNG15
Sequence domains: Uracil DNA glycosylase superfamily

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-31766
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

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