› 3tdu

X-ray diffraction
1.5Å resolution

N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex

Released:
DOI: 10.2210/pdb3tdu/pdb
PDB entry 3tdu coloured by chain, front view.
PDB entry 3tdu coloured by chain, side view.
PDB entry 3tdu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex.
Scott DC, Monda JK, Bennett EJ, Harper JW, Schulman BA
Science 334 674-8 (2011)
PMID: 21940857

Function and Biology Details

Reaction catalysed: 
[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 trimer (preferred)
PDBe Complex ID:
PDB-CPX-548541 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
DCN1-like protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 200 amino acids
Theoretical weight: 23.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96GG9 (Residues: 62-259; Coverage: 76%)
Gene names: DCN1, DCUN1D1, DCUN1L1, RP42, SCCRO
Sequence domains: Cullin binding
Structure domains: EF-hand
Cullin-1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 77 amino acids
Theoretical weight: 9.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13616 (Residues: 702-776; Coverage: 10%)
Gene name: CUL1
Sequence domains: Cullin protein neddylation domain
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
NEDD8-conjugating enzyme Ubc12 Chains: E, F
Molecule details ›
Chains: E, F
Length: 16 amino acids
Theoretical weight: 1.91 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P61081 (Residues: 1-15; Coverage: 8%)
Gene names: UBC12, UBE2M

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: C2
Unit cell:
a: 135.431Å b: 65.454Å c: 64.182Å
α: 90° β: 104.73° γ: 90°
R-values:
R R work R free
0.207 0.206 0.232
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

43 review citations

Protein neddylation: beyond cullin-RING ligases.
Enchev et al. (2015)
42 more

13 mentions without citation

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