› 4p5o

X-ray diffraction
3.11Å resolution

Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action

Released:
DOI: 10.2210/pdb4p5o/pdb
PDB entry 4p5o coloured by chain, front view.
PDB entry 4p5o coloured by chain, side view.
PDB entry 4p5o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of a RING E3 trapped in action reveals ligation mechanism for the ubiquitin-like protein NEDD8.
Scott DC, Sviderskiy VO, Monda JK, Lydeard JR, Cho SE, Harper JW, Schulman BA
Cell 157 1671-84 (2014)
PMID: 24949976

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
[E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine + [E2 NEDD8-conjugating enzyme]-L-cysteine = [E1 NEDD8-activating enzyme]-L-cysteine + [E2 NEDD8-conjugating enzyme]-S-[NEDD8-protein]-yl-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-158196 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Cullin-1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 368 amino acids
Theoretical weight: 42.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13616 (Residues: 410-776; Coverage: 47%)
Gene name: CUL1
Sequence domains:
Structure domains:
E3 ubiquitin-protein ligase RBX1 Chains: B, D
Molecule details ›
Chains: B, D
Length: 106 amino acids
Theoretical weight: 12.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62877 (Residues: 3-108; Coverage: 98%)
Gene names: RBX1, RNF75, ROC1
Sequence domains: RING-H2 zinc finger domain
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
DCN1-like protein 1 Chains: E, F
Molecule details ›
Chains: E, F
Length: 200 amino acids
Theoretical weight: 23.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96GG9 (Residues: 61-259; Coverage: 77%)
Gene names: DCN1, DCUN1D1, DCUN1L1, RP42, SCCRO
Sequence domains: Cullin binding
Structure domains: EF-hand
NEDD8-conjugating enzyme Ubc12 Chains: G, I
Molecule details ›
Chains: G, I
Length: 189 amino acids
Theoretical weight: 21.75 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P61081 (Residues: 2-183; Coverage: 100%)
Gene names: UBC12, UBE2M
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
NEDD8 Chains: H, K
Molecule details ›
Chains: H, K
Length: 81 amino acids
Theoretical weight: 8.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15843 (Residues: 1-76; Coverage: 94%)
Gene name: NEDD8
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 89.105Å b: 129.606Å c: 119.94Å
α: 90° β: 111.79° γ: 90°
R-values:
R R work R free
0.23 0.227 0.284
Expression systems:
  • Escherichia coli
  • Trichoplusia ni

Quick links

Citations

28 review citations

Ubiquitin Ligases: Structure, Function, and Regulation.
Zheng et al. (2017)
27 more

18 mentions without citation

Ubiquitin-like Protein Conjugation: Structures, Chemistry, and Mechanism.
Cappadocia et al. (2018)
17 more