2OOB

crystal structure of the UBA domain from Cbl-b ubiquitin ligase in complex with ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for ubiquitin-mediated dimerization and activation of the ubiquitin protein ligase Cbl-b.

Peschard, P.Kozlov, G.Lin, T.Mirza, I.A.Berghuis, A.M.Lipkowitz, S.Park, M.Gehring, K.

(2007) Mol.Cell 27: 474-485

  • DOI: 10.1016/j.molcel.2007.06.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cbl proteins are E3 ubiquitin ligases that are negative regulators of many receptor tyrosine kinases. Cbl-b and c-Cbl contain a ubiquitin-associated (UBA) domain, which is present in a variety of proteins involved in ubiquitin-mediated processes. Des ...

    Cbl proteins are E3 ubiquitin ligases that are negative regulators of many receptor tyrosine kinases. Cbl-b and c-Cbl contain a ubiquitin-associated (UBA) domain, which is present in a variety of proteins involved in ubiquitin-mediated processes. Despite high sequence identity, Cbl UBA domains display remarkably different ubiquitin-binding properties. Here, we report the crystal structure of the UBA domain of Cbl-b in complex with ubiquitin at 1.9 A resolution. The structure reveals an atypical mechanism of ubiquitin recognition by the first helix of the UBA. Helices 2 and 3 of the UBA domain form a second binding surface, which mediates UBA dimerization in the crystal and in solution. Site-directed mutagenesis demonstrates that Cbl-b dimerization is regulated by ubiquitin binding and required for tyrosine phosphorylation of Cbl-b and ubiquitination of Cbl-b substrates. These studies demonstrate a role for ubiquitin in regulating biological activity by promoting protein dimerization.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montréal, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase CBL-B
A
52Homo sapiensMutation(s): 0 
Gene Names: CBLB (RNF56)
EC: 2.3.2.27
Find proteins for Q13191 (Homo sapiens)
Go to Gene View: CBLB
Go to UniProtKB:  Q13191
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B
76Bos taurusMutation(s): 0 
Gene Names: UBC
Find proteins for P0CH28 (Bos taurus)
Go to Gene View: UBC
Go to UniProtKB:  P0CH28
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 50.608α = 90.00
b = 54.784β = 90.00
c = 94.621γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CrystalCleardata collection
HKL-2000data reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance