› 2hye

X-ray diffraction
3.1Å resolution

Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex

Released:
DOI: 10.2210/pdb2hye/pdb
PDB entry 2hye coloured by chain, front view.
PDB entry 2hye coloured by chain, side view.
PDB entry 2hye coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery.
Angers S, Li T, Yi X, MacCoss MJ, Moon RT, Zheng N
Nature 443 590-3 (2006)
PMID: 16964240

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 domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-145701 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
DNA damage-binding protein 1 Chain: A
Molecule details ›
Chain: A
Length: 1140 amino acids
Theoretical weight: 127.12 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 100%)
Gene names: DDB1, XAP1
Sequence domains:
Structure domains:
Non-structural protein V Chain: B
Molecule details ›
Chain: B
Length: 222 amino acids
Theoretical weight: 23.97 KDa
UniProt:
  • Canonical: P11207 (Residues: 1-222; Coverage: 100%)
Gene name: P/V
Sequence domains:
Cullin-4A Chain: C
Molecule details ›
Chain: C
Length: 759 amino acids
Theoretical weight: 87.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13619 (Residues: 1-759; Coverage: 100%)
Gene name: CUL4A
Sequence domains:
E3 ubiquitin-protein ligase RBX1 Chain: D
Molecule details ›
Chain: D
Length: 108 amino acids
Theoretical weight: 12.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62877 (Residues: 1-108; Coverage: 100%)
Gene names: RBX1, RNF75, ROC1
Sequence domains: RING-H2 zinc finger domain
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

1 bound ligand:
Ligand ZN 5 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: C2221
Unit cell:
a: 83.452Å b: 203.165Å c: 424.875Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.253 0.25 0.316
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli

Quick links

Citations

104 review citations

WD40 proteins propel cellular networks.
Stirnimann et al. (2010)
103 more

36 mentions without citation

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