› 3i8e

X-ray diffraction
3.4Å resolution

Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A

Released:
DOI: 10.2210/pdb3i8e/pdb
PDB entry 3i8e coloured by chain, front view.
PDB entry 3i8e coloured by chain, side view.
PDB entry 3i8e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A promiscuous alpha-helical motif anchors viral hijackers and substrate receptors to the CUL4-DDB1 ubiquitin ligase machinery.
Li T, Robert EI, van Breugel PC, Strubin M, Zheng N
Nat Struct Mol Biol 17 105-11 (2010)
PMID: 19966799

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172474 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
DNA damage-binding protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 1143 amino acids
Theoretical weight: 127.4 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 100%)
Gene names: DDB1, XAP1
Sequence domains:
Structure domains:
DDB1- and CUL4-associated factor 8 Chains: C, D
Molecule details ›
Chains: C, D
Length: 13 amino acids
Theoretical weight: 1.44 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q5TAQ9 (Residues: 153-165; Coverage: 2%)
Gene names: DCAF8, H326, WDR42A

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P21
Unit cell:
a: 64.138Å b: 133.815Å c: 183.999Å
α: 90° β: 90.45° γ: 90°
R-values:
R R work R free
0.304 0.26 0.338
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

45 review citations

Ubiquitin Ligases: Structure, Function, and Regulation.
Zheng et al. (2017)
44 more

2 mentions without citation

Comparative Genomic Characterization of Buffalo Fibronectin Type III Domain Proteins: Exploring the Novel Role of FNDC5/Irisin as a Ligand of Gonadal Receptors.
Wu et al. (2021)
1 more