PDBe 3dqv

X-ray diffraction
3Å resolution

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

Released:

Function and Biology Details

Reactions catalysed:
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
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
Biochemical function:
Cellular component:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero hexamer
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: NEW 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: NEW Q93034 (Residues: 401-780; Coverage: 49%)
Gene names: CUL5, VACM1
Sequence domains: Cullin protein neddylation domain
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: NEW 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:

1 modified residue:

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