Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26433.76 
• Atom Count: 1823 
• Residue Count: 231 
• Unique protein chains: 2

4A49

Structure of phosphoTyr371-c-Cbl-UbcH5B complex

• DOI: 10.2210/pdb4A49/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2011-10-07 Released: 2012-01-25 
• Deposition Author(s): Dou, H., Buetow, L., Hock, A., Sibbet, G.J., Vousden, K.H., Huang, D.T.

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Experimental Data Snapshot

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

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

• PubMed: 22266821 
• DOI: 10.1038/nsmb.2231
• Primary Citation of Related Structures:  
  4A4C, 4A4B, 2Y1N, 2Y1M


• 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, 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
E3 ubiquitin-protein ligase CBL	A	84	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 D2	B	147	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	B	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

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 = 115.877	α = 90.00
b = 115.877	β = 90.00
c = 52.572	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-07 
• Released Date: 2012-01-25 
• Deposition Author(s): Dou, H., Buetow, L., Hock, A., Sibbet, G.J., Vousden, K.H., Huang, D.T.

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