› 3zrh

X-ray diffraction
2.23Å resolution

Crystal structure of the Lys29, Lys33-linkage-specific TRABID OTU deubiquitinase domain reveals an Ankyrin-repeat ubiquitin binding domain (AnkUBD)

Released:
DOI: 10.2210/pdb3zrh/pdb
PDB entry 3zrh coloured by chain, front view.
PDB entry 3zrh coloured by chain, side view.
PDB entry 3zrh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains.
Licchesi JD, Mieszczanek J, Mevissen TE, Rutherford TJ, Akutsu M, Virdee S, El Oualid F, Chin JW, Ovaa H, Bienz M, Komander D
Nat Struct Mol Biol 19 62-71 (2011)
PMID: 22157957

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:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin thioesterase ZRANB1 Chain: A
Molecule details ›
Chain: A
Length: 454 amino acids
Theoretical weight: 52.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9UGI0 (Residues: 245-697; Coverage: 64%)
Gene names: TRABID, ZRANB1
Sequence domains:
Structure domains: Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat

Ligands and Environments

2 bound ligands:
Ligand EDO 2 x EDO
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 60.4Å b: 72.15Å c: 133.01Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.2 0.248
Expression system: Escherichia coli BL21

Quick links

Citations

24 review citations

The ubiquitin code.
Komander et al. (2012)
23 more

5 mentions without citation

An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains.
Licchesi et al. (2011)
4 more