› 4mdk

X-ray diffraction
2.61Å resolution

Cdc34-ubiquitin-CC0651 complex

Released:
DOI: 10.2210/pdb4mdk/pdb
PDB entry 4mdk coloured by chain, front view.
PDB entry 4mdk coloured by chain, side view.
PDB entry 4mdk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin.
Huang H, Ceccarelli DF, Orlicky S, St-Cyr DJ, Ziemba A, Garg P, Plamondon S, Auer M, Sidhu S, Marinier A, Kleiger G, Tyers M, Sicheri F
Nat Chem Biol 10 156-163 (2014)
PMID: 24316736

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143354 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-conjugating enzyme E2 R1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 180 amino acids
Theoretical weight: 20.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P49427 (Residues: 7-184; Coverage: 75%)
Gene names: CDC34, UBCH3, UBE2R1
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 80 amino acids
Theoretical weight: 8.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG48 (Residues: 608-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

1 bound ligand:
Ligand U94 4 x U94
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P1
Unit cell:
a: 55.403Å b: 72.22Å c: 75.912Å
α: 71.89° β: 79.63° γ: 81.61°
R-values:
R R work R free
0.207 0.204 0.259
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

19 review citations

E2 enzymes: more than just middle men.
Stewart et al. (2016)
18 more

12 mentions without citation

Targeting Cullin-RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation.
Bulatov et al. (2015)
11 more