Crystal structure of the catalytic domain of human USP9X

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Crystal structure and activity-based labeling reveal the mechanisms for linkage-specific substrate recognition by deubiquitinase USP9X.

Paudel, P.Zhang, Q.Leung, C.Greenberg, H.C.Guo, Y.Chern, Y.H.Dong, A.Li, Y.Vedadi, M.Zhuang, Z.Tong, Y.

(2019) Proc Natl Acad Sci U S A 116: 7288-7297

  • DOI: https://doi.org/10.1073/pnas.1815027116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    USP9X is a conserved deubiquitinase (DUB) that regulates multiple cellular processes. Dysregulation of USP9X has been linked to cancers and X-linked intellectual disability. Here, we report the crystal structure of the USP9X catalytic domain at 2.5-Å resolution. The structure reveals a canonical USP-fold comprised of fingers, palm, and thumb subdomains, as well as an unusual β-hairpin insertion. The catalytic triad of USP9X is aligned in an active configuration. USP9X is exclusively active against ubiquitin (Ub) but not Ub-like modifiers. Cleavage assays with di-, tri-, and tetraUb chains show that the USP9X catalytic domain has a clear preference for K11-, followed by K63-, K48-, and K6-linked polyUb chains. Using a set of activity-based diUb and triUb probes (ABPs), we demonstrate that the USP9X catalytic domain has an exo-cleavage preference for K48- and endo-cleavage preference for K11-linked polyUb chains. The structure model and biochemical data suggest that the USP9X catalytic domain harbors three Ub binding sites, and a zinc finger in the fingers subdomain and the β-hairpin insertion both play important roles in polyUb chain processing and linkage specificity. Furthermore, unexpected labeling of a secondary, noncatalytic cysteine located on a blocking loop adjacent to the catalytic site by K11-diUb ABP implicates a previously unreported mechanism of polyUb chain recognition. The structural features of USP9X revealed in our study are critical for understanding its DUB activity. The new Ub-based ABPs form a set of valuable tools to understand polyUb chain processing by the cysteine protease class of DUBs.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ubiquitin carboxyl-terminal hydrolase FAF-X
A, B, C, D
421Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q93008 (Homo sapiens)
Explore Q93008 
Go to UniProtKB:  Q93008
PHAROS:  Q93008
GTEx:  ENSG00000124486 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93008
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.372α = 90
b = 79.048β = 103.76
c = 131.933γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.3: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.4: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references, Refinement description