Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 38377.80 
• Atom Count: 2290 
• Residue Count: 344 
• Unique protein chains: 2

3VRO

Crystal structure of the tyrosine kinase binding domain of Cbl-c in complex with phospho-Src peptide

• DOI: 10.2210/pdb3VRO/pdb

• Classification: PROTEIN BINDING/Transferase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2012-04-13 Released: 2013-03-06 
• Deposition Author(s): Takeshita, K., Tezuka, T., Isozaki, Y., Yamashita, E., Suzuki, M., Yamanashi, Y., Yamamoto, T., Nakagawa, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.212 
• R-Value Work: 0.166 

Literature

Structural flexibility regulates phosphopeptide-binding activity of the tyrosine kinase binding domain of Cbl-c.

Takeshita, K., Tezuka, T., Isozaki, Y., Yamashita, E., Suzuki, M., Kim, M., Yamanashi, Y., Yamamoto, T., Nakagawa, A.

(2012) J.Biochem. 152: 487-495

• PubMed: 22888118 
• DOI: 10.1093/jb/mvs085
• Primary Citation of Related Structures:  
  3VRR, 3VRQ, 3VRP, 3VRN


• PubMed Abstract: 
  

Through their ubiquitin ligase activity, Cbl-family proteins suppress signalling mediated by protein-tyrosine kinases (PTKs), but can also function as adaptor proteins to positively regulate signalling. The tyrosine kinase binding (TKB) domain of this family is critical for binding with tyrosine-phosphorylated target proteins. Here, we analysed the crystal structure of the TKB domain of Cbl-c/Cbl-3 (Cbl-c TKB), which is a distinct member of the mammalian Cbl-family. In comparison with Cbl TKB, Cbl-c TKB showed restricted structural flexibility upon phosphopeptide binding. A mutation in Cbl-c TKB augmenting this flexibility enhanced its binding to target phosphoproteins. These results suggest that proteins, post-translational modifications or mutations that alter structural flexibility of the TKB domain of Cbl-family proteins could regulate their binding to target phosphoproteins and thereby, affect PTK-mediated signalling.

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Organizational Affiliation: 

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Signal transduction protein CBL-C	A	331	Homo sapiens	Mutation(s): 0  Gene Names: CBLC (CBL3, RNF57) EC: 2.3.2.27
Find proteins for Q9ULV8 (Homo sapiens) Go to Gene View: CBLC Go to UniProtKB:  Q9ULV8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Proto-oncogene tyrosine-protein kinase Src	B	13	Homo sapiens	Mutation(s): 0  Gene Names: SRC (SRC1) EC: 2.7.10.2
Find proteins for P12931 (Homo sapiens) Go to Gene View: SRC Go to UniProtKB:  P12931

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.212 
• R-Value Work: 0.166 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 93.282	α = 90.00
b = 108.493	β = 90.00
c = 54.761	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-13 
• Released Date: 2013-03-06 
• Deposition Author(s): Takeshita, K., Tezuka, T., Isozaki, Y., Yamashita, E., Suzuki, M., Yamanashi, Y., Yamamoto, T., Nakagawa, A.

Revision History 

• Version 1.0: 2013-03-06
  Type: Initial release
• Version 1.1: 2017-11-22
  Type: Refinement description