› 4orh

X-ray diffraction
4.8Å resolution

Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer

Released:
DOI: 10.2210/pdb4orh/pdb
PDB entry 4orh coloured by chain, front view.
PDB entry 4orh coloured by chain, side view.
PDB entry 4orh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular insights into the function of RING finger (RNF)-containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation.
Campbell SJ, Edwards RA, Leung CC, Neculai D, Hodge CD, Dhe-Paganon S, Glover JN
J Biol Chem 287 23900-10 (2012)
PMID: 22589545

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
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 tetramer
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131198 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 variant 2 Chains: A, E, I
Molecule details ›
Chains: A, E, I
Length: 153 amino acids
Theoretical weight: 17.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q15819 (Residues: 1-145; Coverage: 100%)
Gene names: MMS2, UBE2V2, UEV2
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin-conjugating enzyme E2 N Chains: B, F, J
Molecule details ›
Chains: B, F, J
Length: 160 amino acids
Theoretical weight: 17.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P61088 (Residues: 1-152; Coverage: 100%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme
E3 ubiquitin-protein ligase RNF8 Chains: C, G, H, K, L
Molecule details ›
Chains: C, G, H, K, L
Length: 149 amino acids
Theoretical weight: 17.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O76064 (Residues: 345-485; Coverage: 29%)
Gene names: KIAA0646, RNF8
Sequence domains: Zinc finger, C3HC4 type (RING finger)

Ligands and Environments

1 bound ligand:
Ligand ZN 10 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P42212
Unit cell:
a: 205.258Å b: 205.258Å c: 235.372Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.276 0.276 0.282
Expression system: Escherichia coli BL21

Quick links

Citations

15 review citations

Histone Modifications and Cancer.
Audia et al. (2016)
14 more

5 mentions without citation

Ubc13: the Lys63 ubiquitin chain building machine.
Hodge et al. (2016)
4 more