› 5wch

X-ray diffraction
2.5Å resolution

Crystal structure of the catalytic domain of human USP9X

Released:
DOI: 10.2210/pdb5wch/pdb
PDB entry 5wch coloured by chain, front view.
PDB entry 5wch coloured by chain, side view.
PDB entry 5wch coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure and activity-based labeling reveal the mechanisms for linkage-specific substrate recognition by deubiquitinase USP9X.
Paudel P, Zhang Q, Leung C, Greenberg HC, Guo Y, Chern YH, Dong A, Li Y, Vedadi M, Zhuang Z, Tong Y
Proc Natl Acad Sci U S A 116 7288-7297 (2019)
PMID: 30914461

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:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187972 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin carboxyl-terminal hydrolase 9X Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 421 amino acids
Theoretical weight: 48.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q93008 (Residues: 1551-1970; Coverage: 16%)
Gene names: DFFRX, FAM, USP9, USP9X
Sequence domains: Ubiquitin carboxyl-terminal hydrolase

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand UNX 1 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 79.372Å b: 79.048Å c: 131.933Å
α: 90° β: 103.76° γ: 90°
R-values:
R R work R free
0.208 0.207 0.261
Expression system: Escherichia coli BL21

Quick links

Citations

9 review citations

Post-Translational Modifications of Deubiquitinating Enzymes: Expanding the Ubiquitin Code.
Wang et al. (2021)
8 more

6 mentions without citation

Crystal structure and activity-based labeling reveal the mechanisms for linkage-specific substrate recognition by deubiquitinase USP9X.
Paudel et al. (2019)
5 more