› 4a0k

X-ray diffraction
5.93Å resolution

STRUCTURE OF DDB1-DDB2-CUL4A-RBX1 BOUND TO A 12 BP ABASIC SITE CONTAINING DNA-DUPLEX

Released:
DOI: 10.2210/pdb4a0k/pdb
PDB entry 4a0k coloured by chain, front view.
PDB entry 4a0k coloured by chain, side view.
PDB entry 4a0k 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

Reactions catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]-L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + N(6)-[NEDD8-protein]-yl-[cullin]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-117183 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Cullin-4A Chain: A
Molecule details ›
Chain: A
Length: 742 amino acids
Theoretical weight: 86.7 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13619 (Residues: 38-759; Coverage: 95%)
Gene name: CUL4A
Sequence domains:
E3 ubiquitin-protein ligase RBX1, N-terminally processed Chain: B
Molecule details ›
Chain: B
Length: 117 amino acids
Theoretical weight: 13.63 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P62878 (Residues: 12-108; Coverage: 90%)
Gene name: Rbx1
Sequence domains: RING-H2 zinc finger domain
DNA damage-binding protein 1 Chain: C
Molecule details ›
Chain: C
Length: 1159 amino acids
Theoretical weight: 129.39 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 100%)
Gene names: DDB1, XAP1
Sequence domains:
DNA damage-binding protein 2 Chain: D
Molecule details ›
Chain: D
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
12 BP THF CONTAINING DNA Chain: E
Molecule details ›
Chain: E
Length: 12 nucleotides
Theoretical weight: 3.5 KDa
12 BP DNA Chain: F
Molecule details ›
Chain: F
Length: 12 nucleotides
Theoretical weight: 3.7 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: C2
Unit cell:
a: 210.65Å b: 78.02Å c: 276.62Å
α: 90° β: 108.5° γ: 90°
R-values:
R R work R free
0.269 0.269 0.27
Expression system: Trichoplusia ni

Quick links

Citations

78 review citations

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

18 mentions without citation

Targeted protein degradation as a powerful research tool in basic biology and drug target discovery.
Wu et al. (2020)
17 more