Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 38.38 kDa 
• Atom Count: 2494 
• Modelled Residue Count: 289 
• Deposited 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

• PDB DOI: 10.2210/pdb3VRO/pdb

• Classification: PROTEIN BINDING/Transferase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

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:  
  3VRN, 3VRO, 3VRP, 3VRQ, 3VRR


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal transduction protein CBL-C	A	331	Homo sapiens	Mutation(s): 0  Gene Names: CBLC, CBL3, RNF57 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULV8 (Homo sapiens) Explore Q9ULV8  Go to UniProtKB:  Q9ULV8
PHAROS:  Q9ULV8 GTEx:  ENSG00000142273

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	B	13	Homo sapiens	Mutation(s): 0  Gene Names: SRC, SRC1 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P12931 (Homo sapiens) Explore P12931  Go to UniProtKB:  P12931
PHAROS:  P12931 GTEx:  ENSG00000197122

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth 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: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.282	α = 90
b = 108.493	β = 90
c = 54.761	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
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
  Changes: Refinement description