Crystal structure of human USP25

Experimental Data Snapshot

  • Resolution: 3.28 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


A quaternary tetramer assembly inhibits the deubiquitinating activity of USP25.

Liu, B.Sureda-Gomez, M.Zhen, Y.Amador, V.Reverter, D.

(2018) Nat Commun 9: 4973-4973

  • DOI: https://doi.org/10.1038/s41467-018-07510-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    USP25 deubiquitinating enzyme is a key member of the ubiquitin system, which acts as a positive regulator of the Wnt/β-catenin signaling by promoting the deubiquitination and stabilization of tankyrases. USP25 is characterized by the presence of a long insertion in the middle of the conserved catalytic domain. The crystal structure of USP25 displays an unexpected homotetrameric quaternary assembly that is directly involved in the inhibition of its enzymatic activity. The tetramer is assembled by the association of two dimers and includes contacts between the coiled-coil insertion domain and the ubiquitin-binding pocket at the catalytic domain, revealing a distinctive autoinhibitory mechanism. Biochemical and kinetic assays with dimer, tetramer and truncation constructs of USP25 support this mechanism, displaying higher catalytic activity in the dimer assembly. Moreover, the high stabilization of tankyrases in cultured cells by ectopic expression of a constitutive dimer of USP25 supports a biological relevance of this tetramerization/inhibition mechanism.

  • Organizational Affiliation

    Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 25716Homo sapiensMutation(s): 0 
Gene Names: USP25USP21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHP3 (Homo sapiens)
Explore Q9UHP3 
Go to UniProtKB:  Q9UHP3
GTEx:  ENSG00000155313 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHP3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.28 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.806α = 90
b = 140.806β = 90
c = 190.156γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2015-66417

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references