› 3rpg

X-ray diffraction
2.65Å resolution

Bmi1/Ring1b-UbcH5c complex structure

Released:
DOI: 10.2210/pdb3rpg/pdb
PDB entry 3rpg coloured by chain, front view.
PDB entry 3rpg coloured by chain, side view.
PDB entry 3rpg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex.
Bentley ML, Corn JE, Dong KC, Phung Q, Cheung TK, Cochran AG
EMBO J 30 3285-97 (2011)
PMID: 21772249

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
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:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
hetero dimer
PDBe Complex ID:
PDB-CPX-152854 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 D3 Chain: A
Molecule details ›
Chain: A
Length: 149 amino acids
Theoretical weight: 16.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61077 (Residues: 2-147; Coverage: 99%)
Gene names: UBC5C, UBCH5C, UBE2D3
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Polycomb complex protein BMI-1 Chain: B
Molecule details ›
Chain: B
Length: 117 amino acids
Theoretical weight: 13.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P35226 (Residues: 1-109; Coverage: 33%)
Gene names: BMI1, PCGF4, RNF51
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
E3 ubiquitin-protein ligase RING2 Chain: C
Molecule details ›
Chain: C
Length: 121 amino acids
Theoretical weight: 13.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99496 (Residues: 1-116; Coverage: 35%)
Gene names: BAP1, DING, HIPI3, RING1B, RNF2
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P3221
Unit cell:
a: 107.89Å b: 107.89Å c: 77.572Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.219 0.217 0.243
Expression system: Escherichia coli

Quick links

Citations

30 review citations

The ubiquitin code.
Komander et al. (2012)
29 more

18 mentions without citation

Specificity and disease in the ubiquitin system.
Chaugule et al. (2016)
17 more