› 4whv

X-ray diffraction
8.3Å resolution

E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B

Released:
DOI: 10.2210/pdb4whv/pdb
PDB entry 4whv coloured by chain, front view.
PDB entry 4whv coloured by chain, side view.
PDB entry 4whv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment.
Hodge CD, Ismail IH, Edwards RA, Hura GL, Xiao AT, Tainer JA, Hendzel MJ, Glover JN
J Biol Chem 291 9396-410 (2016)
PMID: 26903517

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

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-131201 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 N Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 160 amino acids
Theoretical weight: 17.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61088 (Residues: 1-152; Coverage: 100%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme
E3 ubiquitin-protein ligase RNF8 Chains: C, D, I, J
Molecule details ›
Chains: C, D, I, J
Length: 149 amino acids
Theoretical weight: 17.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O76064 (Residues: 345-485; Coverage: 29%)
Gene names: KIAA0646, RNF8
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Ubiquitin Chains: A, F, G, L
Molecule details ›
Chains: A, F, G, L
Length: 83 amino acids
Theoretical weight: 9.29 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:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P6422
Unit cell:
a: 341.379Å b: 341.379Å c: 113.447Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.33 0.329 0.337
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

8 review citations

Ubiquitin-like Protein Conjugation: Structures, Chemistry, and Mechanism.
Cappadocia et al. (2018)
7 more

3 mentions without citation

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