› 5vey

Solution NMR

Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A Lys15 in complex with RNF169 (653-708)

Released:
DOI: 10.2210/pdb5vey/pdb
PDB entry 5vey coloured by chain, ensemble of 20 models, front view.
PDB entry 5vey coloured by chain, ensemble of 20 models, side view.
PDB entry 5vey coloured by chain, ensemble of 20 models, top view.
Source organism: Homo sapiens
Primary publication:
Mechanisms of Ubiquitin-Nucleosome Recognition and Regulation of 53BP1 Chromatin Recruitment by RNF168/169 and RAD18.
Hu Q, Botuyan MV, Cui G, Zhao D, Mer G
Mol Cell 66 473-487.e9 (2017)
PMID: 28506460

Function and Biology Details

Reaction 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
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-138256 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Histone H2A type 1-B/E; Histone H2B type 1-J Chain: A
Molecule details ›
Chain: A
Length: 194 amino acids
Theoretical weight: 21.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06899 (Residues: 34-124; Coverage: 72%)
  • Canonical: P04908 (Residues: 13-13, 15-106; Coverage: 72%)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, H2BC11, H2BFR, HIST1H2AB, HIST1H2AE, HIST1H2BJ
Sequence domains:
Structure domains: Histone, subunit A
Ubiquitin Chain: B
Molecule details ›
Chain: B
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
E3 ubiquitin-protein ligase RNF169 Chain: C
Molecule details ›
Chain: C
Length: 59 amino acids
Theoretical weight: 7.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8NCN4 (Residues: 653-708; Coverage: 8%)
Gene names: KIAA1991, RNF169

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Chemical shift assignment: 82%
Refinement method: simulated annealing
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

19 review citations

How cells ensure correct repair of DNA double-strand breaks.
Her et al. (2018)
18 more

1 mention without citation

Mechanisms of Ubiquitin-Nucleosome Recognition and Regulation of 53BP1 Chromatin Recruitment by RNF168/169 and RAD18.
Hu et al. (2017)