4a0k

X-ray diffraction
5.93Å resolution

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

Released:

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:

Structure analysis Details

Assembly composition:
hetero hexamer (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