› 3dqv

X-ray diffraction
3Å resolution

Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation

Released:
DOI: 10.2210/pdb3dqv/pdb
PDB entry 3dqv coloured by chain, front view.
PDB entry 3dqv coloured by chain, side view.
PDB entry 3dqv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation.
Duda DM, Borg LA, Scott DC, Hunt HW, Hammel M, Schulman BA
Cell 134 995-1006 (2008)
PMID: 18805092

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

Assemblies composition:
hetero trimer (preferred)
hetero hexamer
PDBe Complex ID:
PDB-CPX-158750 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
NEDD8 Chains: A, B
Molecule details ›
Chains: A, B
Length: 81 amino acids
Theoretical weight: 9.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15843 (Residues: 1-76; Coverage: 94%)
Gene name: NEDD8
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Cullin-5 Chains: C, D
Molecule details ›
Chains: C, D
Length: 382 amino acids
Theoretical weight: 45.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93034 (Residues: 401-780; Coverage: 49%)
Gene names: CUL5, VACM1
Sequence domains:
Structure domains:
E3 ubiquitin-protein ligase RBX1 Chains: R, Y
Molecule details ›
Chains: R, Y
Length: 106 amino acids
Theoretical weight: 12.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62877 (Residues: 5-108; Coverage: 96%)
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 6 x ZN
1 modified residue:
Ligand MSE 36 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P212121
Unit cell:
a: 88.315Å b: 122.442Å c: 128.647Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.249 0.249 0.299
Expression system: Escherichia coli

Quick links

Citations

136 review citations

RING domain E3 ubiquitin ligases.
Deshaies et al. (2009)
135 more

26 mentions without citation

Anticancer drug discovery by targeting cullin neddylation.
Yu et al. (2020)
25 more