PDBe 5ait

X-ray diffraction
3.4Å resolution

A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink)

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. 
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ubiquitin Chains: C, F
Molecule details ›
Chains: C, F
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Bos taurus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CH28 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
E3 ubiquitin-protein ligase RNF4 Chain: A
Molecule details ›
Chain: A
Length: 133 amino acids
Theoretical weight: 14.76 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: O88846 (Residues: 131-194; Coverage: 33%)
Gene names: Rnf4, Snurf
Sequence domains: Ring finger domain
Ubiquitin-conjugating enzyme E2 N Chains: B, E
Molecule details ›
Chains: B, E
Length: 154 amino acids
Theoretical weight: 17.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61088 (Residues: 1-152; Coverage: 100%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin-conjugating enzyme E2 variant 2 Chains: D, G
Molecule details ›
Chains: D, G
Length: 147 amino acids
Theoretical weight: 16.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15819 (Residues: 1-145; Coverage: 100%)
Gene names: MMS2, UBE2V2, UEV2
Sequence domains: Ubiquitin-conjugating enzyme

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P3221
Unit cell:
a: 77.58Å b: 77.58Å c: 328.84Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.208 0.286
Expression system: Escherichia coli