6CRN

Structure of the USP15 deubiquitinase domain in complex with a high-affinity first-generation Ubv


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15.

Teyra, J.Singer, A.U.Schmitges, F.W.Jaynes, P.Kit Leng Lui, S.Polyak, M.J.Fodil, N.Krieger, J.R.Tong, J.Schwerdtfeger, C.Brasher, B.B.Ceccarelli, D.F.J.Moffat, J.Sicheri, F.Moran, M.F.Gros, P.Eichhorn, P.J.A.Lenter, M.Boehmelt, G.Sidhu, S.S.

(2019) Structure 27: 590

  • DOI: 10.1016/j.str.2019.01.002
  • Primary Citation of Related Structures:  
    6DJ9, 6CPM, 6CRN, 6ML1

  • PubMed Abstract: 
  • The multi-domain deubiquitinase USP15 regulates diverse eukaryotic processes and has been implicated in numerous diseases. We developed ubiquitin variants (UbVs) that targeted either the catalytic domain or each of three adaptor domains in USP15, includi ...

    The multi-domain deubiquitinase USP15 regulates diverse eukaryotic processes and has been implicated in numerous diseases. We developed ubiquitin variants (UbVs) that targeted either the catalytic domain or each of three adaptor domains in USP15, including the N-terminal DUSP domain. We also designed a linear dimer (diUbV), which targeted the DUSP and catalytic domains, and exhibited enhanced specificity and more potent inhibition of catalytic activity than either UbV alone. In cells, the UbVs inhibited the deubiquitination of two USP15 substrates, SMURF2 and TRIM25, and the diUbV inhibited the effects of USP15 on the transforming growth factor β pathway. Structural analyses revealed that three distinct UbVs bound to the catalytic domain and locked the active site in a closed, inactive conformation, and one UbV formed an unusual strand-swapped dimer and bound two DUSP domains simultaneously. These inhibitors will enable the study of USP15 function in oncology, neurology, immunology, and inflammation.


    Organizational Affiliation

    The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: sachdev.sidhu@utoronto.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 15 ABCD360Homo sapiensMutation(s): 0 
Gene Names: USP15KIAA0529
EC: 3.4.19.12
Find proteins for Q9Y4E8 (Homo sapiens)
Explore Q9Y4E8 
Go to UniProtKB:  Q9Y4E8
NIH Common Fund Data Resources
PHAROS:  Q9Y4E8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin variant 15.2 EFGH81Homo sapiensMutation(s): 0 
Gene Names: Ubb
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.77α = 66.49
b = 98.942β = 88.31
c = 122.043γ = 78.1
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-17
    Changes: Data collection, Database references