› 5xiu

X-ray diffraction
1.8Å resolution

Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin

Released:
DOI: 10.2210/pdb5xiu/pdb
PDB entry 5xiu coloured by chain, front view.
PDB entry 5xiu coloured by chain, side view.
PDB entry 5xiu coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.
Takahashi TS, Hirade Y, Toma A, Sato Y, Yamagata A, Goto-Ito S, Tomita A, Nakada S, Fukai S
Nat Commun 9 170 (2018)
PMID: 29330428

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158830 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase RNF168 Chain: A
Molecule details ›
Chain: A
Length: 49 amino acids
Theoretical weight: 5.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IYW5 (Residues: 419-462; Coverage: 8%)
Gene name: RNF168
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P62983 (Residues: 1-76; Coverage: 49%)
Gene names: Rps27a, Uba80, Ubcep1
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand EDO 5 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21212
Unit cell:
a: 59.442Å b: 78.548Å c: 31.015Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.169 0.207
Expression system: Escherichia coli

Quick links

Citations

3 review citations

The role of ubiquitination in tumorigenesis and targeted drug discovery.
Deng et al. (2020)
2 more

2 mentions without citation

New answers to the old RIDDLE: RNF168 and the DNA damage response pathway.
Kelliher et al. (2022)
1 more