› 4bos

X-ray diffraction
2.35Å resolution

Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide

Released:
DOI: 10.2210/pdb4bos/pdb
PDB entry 4bos coloured by chain, front view.
PDB entry 4bos coloured by chain, side view.
PDB entry 4bos coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis.
Mevissen TE, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SM, Ovaa H, Komander D
Cell 154 169-84 (2013)
PMID: 23827681

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143335 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin thioesterase OTU1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 169 amino acids
Theoretical weight: 19.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5VVQ6 (Residues: 147-314; Coverage: 48%)
Gene names: DUBA8, HIN7, OTUD2, PRO0907, YOD1
Sequence domains: OTU-like cysteine protease
Structure domains: Cathepsin B; Chain A
Ubiquitin Chains: C, E
Molecule details ›
Chains: C, E
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Ubiquitin Chain: F
Molecule details ›
Chain: F
Length: 14 amino acids
Theoretical weight: 1.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG48 (Residues: 612-625; Coverage: 2%)
Gene name: UBC

Ligands and Environments

2 bound ligands:
Ligand NO3 5 x NO3
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P6
Unit cell:
a: 164.48Å b: 164.48Å c: 44.73Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.189 0.187 0.238
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

102 review citations

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

5 mentions without citation

A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase.
Jupin et al. (2017)
4 more