PDBe 5edv

X-ray diffraction
3.48Å resolution

Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex

Released:

Function and Biology Details

Reactions catalysed:
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
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
Cellular component:

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
hetero octamer
monomeric
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase RNF31 Chains: A, B
Molecule details ›
Chains: A, B
Length: 380 amino acids
Theoretical weight: 43.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96EP0 (Residues: 696-1072; Coverage: 35%)
Gene names: RNF31, ZIBRA
Sequence domains:
Ubiquitin-conjugating enzyme E2 D2 Chains: C, D, I
Molecule details ›
Chains: C, D, I
Length: 149 amino acids
Theoretical weight: 16.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 2-147; Coverage: 99%)
  • Best match: P62837-2 (Residues: 1-118)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21
Unit cell:
a: 104.82Å b: 75.74Å c: 120.96Å
α: 90° β: 95.56° γ: 90°
R-values:
R R work R free
0.251 0.249 0.303
Expression system: Escherichia coli