› 3ei1

X-ray diffraction
2.8Å resolution

Structure of hsDDB1-drDDB2 bound to a 14 bp 6-4 photoproduct containing DNA-duplex

Released:
DOI: 10.2210/pdb3ei1/pdb
PDB entry 3ei1 coloured by chain, front view.
PDB entry 3ei1 coloured by chain, side view.
PDB entry 3ei1 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-116207 (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*DCP*DGP*DCP*DGP*DAP*(64T)P*(5PY)P*DGP*DCP*DGP*DCP*DCP*DC)-3' Chain: G
Molecule details ›
Chain: G
Length: 14 nucleotides
Theoretical weight: 4.24 KDa
5'-D(*DTP*DGP*DGP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DCP*DGP*DCP*DG)-3' Chain: H
Molecule details ›
Chain: H
Length: 14 nucleotides
Theoretical weight: 4.32 KDa

Ligands and Environments

1 bound ligand:
Ligand PG4 1 x PG4
2 modified residues:
Ligand 64T 1 x 64T
Ligand 5PY 1 x 5PY

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 112.74Å b: 123.6Å c: 158.37Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.22 0.278
Expression system: Trichoplusia ni

Quick links

Citations

77 review citations

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

13 mentions without citation

XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase.
Fuss et al. (2011)
12 more