› 5gg4

X-ray diffraction
3.11Å resolution

Crystal structure of USP7 with RNF169 peptide

Released:
DOI: 10.2210/pdb5gg4/pdb
PDB entry 5gg4 coloured by chain, front view.
PDB entry 5gg4 coloured by chain, side view.
PDB entry 5gg4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Dual-utility NLS drives RNF169-dependent DNA damage responses.
An L, Jiang Y, Ng HH, Man EP, Chen J, Khoo US, Gong Q, Huen MS
Proc Natl Acad Sci U S A 114 E2872-E2881 (2017)
PMID: 28325877

Function and Biology Details

Reactions catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
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 domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185491 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin carboxyl-terminal hydrolase 7 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 334 amino acids
Theoretical weight: 38.87 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q93009 (Residues: 560-890; Coverage: 30%)
Gene names: HAUSP, USP7
Sequence domains: ICP0-binding domain of Ubiquitin-specific protease 7
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
E3 ubiquitin-protein ligase RNF169 Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 13 amino acids
Theoretical weight: 1.66 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q8NCN4 (Residues: 620-632; Coverage: 2%)
Gene names: KIAA1991, RNF169

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: C2
Unit cell:
a: 162.195Å b: 99.965Å c: 124.299Å
α: 90° β: 95.54° γ: 90°
R-values:
R R work R free
0.228 0.226 0.268
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

13 review citations

Molecular Mechanisms of DUBs Regulation in Signaling and Disease.
Li et al. (2021)
12 more

4 mentions without citation

USP7: Structure, substrate specificity, and inhibition.
Pozhidaeva et al. (2019)
3 more