5jk7

X-ray diffraction
3.49Å resolution

The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex

Released:

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:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-146252 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
DNA damage-binding protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 1140 amino acids
Theoretical weight: 127.1 KDa
Source organism: Homo sapiens
Expression system: Insect cell expression vector pTIE1
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 100%)
Gene names: DDB1, XAP1
Sequence domains:
Structure domains:
DDB1- and CUL4-associated factor 1 Chains: C, E
Molecule details ›
Chains: C, E
Length: 361 amino acids
Theoretical weight: 41.18 KDa
Source organism: Homo sapiens
Expression system: Insect cell expression vector pTIE1
UniProt:
  • Canonical: Q9Y4B6 (Residues: 1045-1396; Coverage: 23%)
Gene names: DCAF1, KIAA0800, RIP, VPRBP
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Uracil-DNA glycosylase Chains: D, G
Molecule details ›
Chains: D, G
Length: 222 amino acids
Theoretical weight: 25.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
UniProt:
  • Canonical: P13051 (Residues: 94-313; Coverage: 70%)
Gene names: DGU, UNG, UNG1, UNG15
Sequence domains: Uracil DNA glycosylase superfamily
Structure domains: Uracil-DNA glycosylase-like domain
Protein Vpr Chains: F, H
Molecule details ›
Chains: F, H
Length: 96 amino acids
Theoretical weight: 11.4 KDa
Source organism: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
UniProt:
  • Canonical: P12520 (Residues: 1-96; Coverage: 100%)
Gene name: vpr
Sequence domains: VPR/VPX protein
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P1
Unit cell:
a: 119.9Å b: 128.2Å c: 129.2Å
α: 75.11° β: 89.44° γ: 65.37°
R-values:
R R work R free
0.177 0.176 0.206
Expression systems:
  • Insect cell expression vector pTIE1
  • Escherichia coli-Pichia pastoris shuttle vector pPpARG4