Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.23 kDa 
• Atom Count: 1058 
• Modelled Residue Count: 116 
• Deposited Residue Count: 128 
• Unique protein chains: 2

2OOB

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

• DOI: 10.2210/pdb2OOB/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens, Bos taurus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-01-25 Released: 2007-02-06 
• Deposition Author(s): Kozlov, G., Gehring, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

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

• PubMed: 17679095 
• DOI: 10.1016/j.molcel.2007.06.023
• Primary Citation of Related Structures:  
  2OOB, 2OOA


• 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. 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.

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Organizational Affiliation: 

Department of Biochemistry, McGill University, Montréal, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CBL-B	A	52	Homo sapiens	Mutation(s): 0  Gene Names: CBLB, RNF56, Nbla00127 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q13191 (Homo sapiens) Explore Q13191  Go to UniProtKB:  Q13191
NIH Common Fund Data Resources
PHAROS:  Q13191 GTEx:  ENSG00000114423

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	76	Bos taurus	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CH28 (Bos taurus) Explore P0CH28  Go to UniProtKB:  P0CH28

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.608	α = 90
b = 54.784	β = 90
c = 94.621	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-25 
• Released Date: 2007-02-06 
Deposition Author(s): Kozlov, G., Gehring, K.

Revision History  

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