3tdz

X-ray diffraction
2Å resolution

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

Released:

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-158199 (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: 13 amino acids
Theoretical weight: 1.55 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P61081 (Residues: 1-12; Coverage: 7%)
Gene names: UBC12, UBE2M

Ligands and Environments

No bound ligands
2 modified residues:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2221
Unit cell:
a: 131.79Å b: 190.21Å c: 67.506Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.196 0.224
Expression systems:
  • Escherichia coli
  • Not provided