4A49

Structure of phosphoTyr371-c-Cbl-UbcH5B complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.214 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history. 

Literature

Structural basis for autoinhibition and phosphorylation-dependent activation of c-Cbl.

Dou, H., Buetow, L., Hock, A., Sibbet, G.J., Vousden, K.H., Huang, D.T.

(2012) Nat. Struct. Mol. Biol. 19: 184-192

  • DOI: 10.1038/nsmb.2231
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Cbls are RING ubiquitin ligases that attenuate receptor tyrosine kinase (RTK) signal transduction. Cbl ubiquitination activity is stimulated by phosphorylation of a linker helix region (LHR) tyrosine residue. To elucidate the mechanism of activation, ...

    Cbls are RING ubiquitin ligases that attenuate receptor tyrosine kinase (RTK) signal transduction. Cbl ubiquitination activity is stimulated by phosphorylation of a linker helix region (LHR) tyrosine residue. To elucidate the mechanism of activation, we determined the structures of human CBL, a CBL-substrate peptide complex and a phosphorylated-Tyr371-CBL-E2-substrate peptide complex, and we compared them with the known structure of a CBL-E2-substrate peptide complex. Structural and biochemical analyses show that CBL adopts an autoinhibited RING conformation, where the RING's E2-binding surface associates with CBL to reduce E2 affinity. Tyr371 phosphorylation activates CBL by inducing LHR conformational changes that eliminate autoinhibition, flip the RING domain and E2 into proximity of the substrate-binding site and transform the RING domain into an enhanced E2-binding module. This activation is required for RTK ubiquitination. Our results present a mechanism for regulation of c-Cbl's activity by autoinhibition and phosphorylation-induced activation.

    Organizational Affiliation: 

    The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow, G61 1BD, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase CBL
A
84Homo sapiensMutation(s): 1 
Gene Names: CBL (CBL2, RNF55)
EC: 2.3.2.27
Find proteins for P22681 (Homo sapiens)
Go to Gene View: CBL
Go to UniProtKB:  P22681
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 D2
B
147Homo sapiensMutation(s): 0 
Gene Names: UBE2D2 (PUBC1, UBC4, UBC5B, UBCH4, UBCH5B)
EC: 2.3.2.23
Find proteins for P62837 (Homo sapiens)
Go to Gene View: UBE2D2
Go to UniProtKB:  P62837
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.214 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.168 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.877α = 90.00
b = 115.877β = 90.00
c = 52.572γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-02-29
    Type: Other
  • Version 2.0: 2018-11-21
    Type: Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Source and taxonomy, Structure summary