3V6E

Crystal Structure of USP2 and a mutant form of Ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A strategy for modulation of enzymes in the ubiquitin system.

Ernst, A.Avvakumov, G.Tong, J.Fan, Y.Zhao, Y.Alberts, P.Persaud, A.Walker, J.R.Neculai, A.M.Neculai, D.Vorobyov, A.Garg, P.Beatty, L.Chan, P.K.Juang, Y.C.Landry, M.C.Yeh, C.Zeqiraj, E.Karamboulas, K.Allali-Hassani, A.Vedadi, M.Tyers, M.Moffat, J.Sicheri, F.Pelletier, L.Durocher, D.Raught, B.Rotin, D.Yang, J.Moran, M.F.Dhe-Paganon, S.Sidhu, S.S.

(2013) Science 339: 590-595

  • DOI: 10.1126/science.1230161
  • Primary Citation of Related Structures:  
    3N3K, 3MTN, 4I6L, 3I3T, 3V6E

  • PubMed Abstract: 
  • The ubiquitin system regulates virtually all aspects of cellular function. We report a method to target the myriad enzymes that govern ubiquitination of protein substrates. We used massively diverse combinatorial libraries of ubiquitin variants to de ...

    The ubiquitin system regulates virtually all aspects of cellular function. We report a method to target the myriad enzymes that govern ubiquitination of protein substrates. We used massively diverse combinatorial libraries of ubiquitin variants to develop inhibitors of four deubiquitinases (DUBs) and analyzed the DUB-inhibitor complexes with crystallography. We extended the selection strategy to the ubiquitin conjugating (E2) and ubiquitin ligase (E3) enzymes and found that ubiquitin variants can also enhance enzyme activity. Last, we showed that ubiquitin variants can bind selectively to ubiquitin-binding domains. Ubiquitin variants exhibit selective function in cells and thus enable orthogonal modulation of specific enzymatic steps in the ubiquitin system.


    Organizational Affiliation

    Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 2A367Homo sapiensMutation(s): 0 
Gene Names: UBP41usp02.258.605USP2
EC: 3.4.19.12
Find proteins for O75604 (Homo sapiens)
Explore O75604 
Go to UniProtKB:  O75604
NIH Common Fund Data Resources
PHAROS  O75604
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB91Homo sapiensMutation(s): 4 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.097α = 90
b = 84.124β = 90
c = 87.371γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references
  • Version 1.2: 2013-08-14
    Changes: Structure summary
  • Version 1.3: 2017-11-08
    Changes: Refinement description