› 4a09

X-ray diffraction
3.1Å resolution

Structure of hsDDB1-drDDB2 bound to a 15 bp CPD-duplex (purine at D-1 position) at 3.1 A resolution (CPD 2)

Released:
DOI: 10.2210/pdb4a09/pdb
PDB entry 4a09 coloured by chain, front view.
PDB entry 4a09 coloured by chain, side view.
PDB entry 4a09 coloured by chain, top view.
Source organisms:
Primary publication:
The molecular basis of CRL4DDB2/CSA ubiquitin ligase architecture, targeting, and activation.
Fischer ES, Scrima A, Böhm K, Matsumoto S, Lingaraju GM, Faty M, Yasuda T, Cavadini S, Wakasugi M, Hanaoka F, Iwai S, Gut H, Sugasawa K, Thomä NH
Cell 147 1024-39 (2011)
PMID: 22118460

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-117180 (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: 1159 amino acids
Theoretical weight: 129.34 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: 382 amino acids
Theoretical weight: 43.42 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(*GP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*GP)-3' Chain: G
Molecule details ›
Chain: G
Length: 14 nucleotides
Theoretical weight: 4.7 KDa
5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3' Chain: H
Molecule details ›
Chain: H
Length: 16 nucleotides
Theoretical weight: 4.72 KDa

Ligands and Environments

1 bound ligand:
Ligand CA 1 x CA
1 modified residue:
Ligand TTD 1 x TTD

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 111.65Å b: 122.94Å c: 154.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.248 0.245 0.308
Expression system: Trichoplusia ni

Quick links

Citations

81 review citations

Induced protein degradation: an emerging drug discovery paradigm.
Lai et al. (2017)
80 more

3 mentions without citation

Xeroderma pigmentosum group C sensor: unprecedented recognition strategy and tight spatiotemporal regulation.
Puumalainen et al. (2016)
2 more