PDBe 3rpg

X-ray diffraction
2.65Å resolution

Bmi1/Ring1b-UbcH5c complex structure

Released:

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:
Cellular component:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
hetero dimer
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:

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