› 6zue

X-ray diffraction
3.09Å resolution

Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-1396)

Released:
DOI: 10.2210/pdb6zue/pdb
PDB entry 6zue coloured by chain, front view.
PDB entry 6zue coloured by chain, side view.
PDB entry 6zue coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses.
Banchenko S, Krupp F, Gotthold C, Bürger J, Graziadei A, O'Reilly FJ, Sinn L, Ruda O, Rappsilber J, Spahn CMT, Mielke T, Taylor IA, Schwefel D
OpenAccess logo PLoS Pathog 17 e1009775 (2021)
PMID: 34339457

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172485 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
DNA damage-binding protein 1 Chain: A
Molecule details ›
Chain: A
Length: 1142 amino acids
Theoretical weight: 127.24 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 100%)
Gene names: DDB1, XAP1
Sequence domains:
DDB1- and CUL4-associated factor 1 Chain: B
Molecule details ›
Chain: B
Length: 373 amino acids
Theoretical weight: 42.5 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9Y4B6 (Residues: 1045-1396; Coverage: 23%)
Gene names: DCAF1, KIAA0800, RIP, VPRBP

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: I222
Unit cell:
a: 117.384Å b: 153.626Å c: 223.156Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.225 0.222 0.279
Expression system: Spodoptera frugiperda

Quick links

Citations

5 citation in other articles

Targeted Protein Degradation by Electrophilic PROTACs that Stereoselectively and Site-Specifically Engage DCAF1.
Tao et al. (2022)
4 more

3 mentions without citation

Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses.
Banchenko et al. (2021)
2 more