› 3wxf

X-ray diffraction
2.3Å resolution

Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin

Released:
DOI: 10.2210/pdb3wxf/pdb
PDB entry 3wxf coloured by chain, front view.
PDB entry 3wxf coloured by chain, side view.
PDB entry 3wxf 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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123083 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin carboxyl-terminal hydrolase CYLD Chains: A, C
Molecule details ›
Chains: A, C
Length: 312 amino acids
Theoretical weight: 35.99 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, D
Molecule details ›
Chains: B, D
Length: 148 amino acids
Theoretical weight: 16.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 533-680; Coverage: 22%)
Gene name: UBC
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P1
Unit cell:
a: 49.628Å b: 65.372Å c: 69.846Å
α: 77.66° β: 89.04° γ: 89.46°
R-values:
R R work R free
0.189 0.187 0.228
Expression system: Escherichia coli

Quick links

Citations

40 review citations

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

1 mention without citation

Substrate specificity of the ubiquitin and Ubl proteases.
Ronau et al. (2016)