› 3wxg

X-ray diffraction
3.1Å resolution

Crystal structure of CYLD USP domain (C596A) in complex with Lys63-linked diubiquitin

Released:
DOI: 10.2210/pdb3wxg/pdb
PDB entry 3wxg coloured by chain, front view.
PDB entry 3wxg coloured by chain, side view.
PDB entry 3wxg coloured by chain, top view.
Source organisms:
Primary publication:
Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.
Sato Y, Goto E, Shibata Y, Kubota Y, Yamagata A, Goto-Ito S, Kubota K, Inoue J, Takekawa M, Tokunaga F, Fukai S
Nat Struct Mol Biol 22 222-9 (2015)
PMID: 25686088

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123084 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin carboxyl-terminal hydrolase CYLD Chains: A, D
Molecule details ›
Chains: A, D
Length: 312 amino acids
Theoretical weight: 35.98 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: E7FEV5 (Residues: 578-780, 850-951; Coverage: 32%)
Gene name: cylda
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: Cysteine proteinases
Ubiquitin Chains: B, E
Molecule details ›
Chains: B, E
Length: 76 amino acids
Theoretical weight: 8.6 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG50 (Residues: 609-684; Coverage: 10%)
Gene name: Ubc
Sequence domains: Ubiquitin family
Ubiquitin Chains: C, F
Molecule details ›
Chains: C, F
Length: 72 amino acids
Theoretical weight: 8.19 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG50 (Residues: 609-680; Coverage: 10%)
Gene name: Ubc
Sequence domains: Ubiquitin family

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P1
Unit cell:
a: 50.017Å b: 65.657Å c: 69.821Å
α: 103.49° β: 89.86° γ: 90.61°
R-values:
R R work R free
0.191 0.188 0.246
Expression system: Escherichia coli

Quick links

Citations

39 review citations

Ubiquitin modifications.
Swatek et al. (2016)
38 more

5 mentions without citation

Protein Engineering in the Ubiquitin System: Tools for Discovery and Beyond.
Zhao et al. (2020)
4 more