› 4s3o

X-ray diffraction
2Å resolution

PCGF5-RING1B-UbcH5c complex

Released:
DOI: 10.2210/pdb4s3o/pdb
PDB entry 4s3o coloured by chain, front view.
PDB entry 4s3o coloured by chain, side view.
PDB entry 4s3o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
BMI1-RING1B is an autoinhibited RING E3 ubiquitin ligase.
Taherbhoy AM, Huang OW, Cochran AG
Nat Commun 6 7621 (2015)
PMID: 26151332

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

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-158195 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 D3 Chains: A, D
Molecule details ›
Chains: A, D
Length: 148 amino acids
Theoretical weight: 16.72 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
E3 ubiquitin-protein ligase RING2 Chains: B, E
Molecule details ›
Chains: B, E
Length: 118 amino acids
Theoretical weight: 13.25 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)
Polycomb group RING finger protein 5 Chains: C, F
Molecule details ›
Chains: C, F
Length: 117 amino acids
Theoretical weight: 13.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q86SE9 (Residues: 1-109; Coverage: 43%)
Gene names: PCGF5, RNF159
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 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 54.392Å b: 105.285Å c: 132.417Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.194 0.237
Expression system: Escherichia coli

Quick links

Citations

24 review citations

Molecular architecture of polycomb repressive complexes.
Chittock et al. (2017)
23 more

1 mention without citation

The structure of the cysteine-rich region from human histone-lysine N-methyltransferase EHMT2 (G9a).
Kerchner et al. (2021)