› 3ei2

X-ray diffraction
2.6Å resolution

Structure of hsDDB1-drDDB2 bound to a 16 bp abasic site containing DNA-duplex

Released:
DOI: 10.2210/pdb3ei2/pdb
PDB entry 3ei2 coloured by chain, front view.
PDB entry 3ei2 coloured by chain, side view.
PDB entry 3ei2 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex.
Scrima A, Konícková R, Czyzewski BK, Kawasaki Y, Jeffrey PD, Groisman R, Nakatani Y, Iwai S, Pavletich NP, Thomä NH
Cell 135 1213-23 (2008)
PMID: 19109893

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-116208 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA damage-binding protein 1 Chain: A
Molecule details ›
Chain: A
Length: 1158 amino acids
Theoretical weight: 129.25 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 100%)
Gene names: DDB1, XAP1
Sequence domains:
Structure domains:
DNA damage-binding protein 2 Chain: B
Molecule details ›
Chain: B
Length: 383 amino acids
Theoretical weight: 43.56 KDa
Source organism: Danio rerio
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q2YDS1 (Residues: 60-423; Coverage: 73%)
Gene names: ddb2, si:dkey-45f10.3
Sequence domains: WD domain, G-beta repeat
Structure domains:
5'-D(*DAP*DAP*DAP*DTP*DGP*DAP*DAP*DTP*(3DR)P*DAP*DAP*DGP*DCP*DAP*DGP*DG)-3' Chain: G
Molecule details ›
Chain: G
Length: 16 nucleotides
Theoretical weight: 4.86 KDa
5'-D(*DCP*DCP*DTP*DGP*DCP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP*DTP*DT)-3' Chain: H
Molecule details ›
Chain: H
Length: 16 nucleotides
Theoretical weight: 4.81 KDa

Ligands and Environments

1 bound ligand:
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 113.21Å b: 123.48Å c: 159.79Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.22 0.268
Expression system: Trichoplusia ni

Quick links

Citations

81 review citations

Mechanisms of DNA damage, repair, and mutagenesis.
Chatterjee et al. (2017)
80 more

6 mentions without citation

Mechanism of CRL4(Cdt2), a PCNA-dependent E3 ubiquitin ligase.
Havens et al. (2011)
5 more