6C4S

Human cSrc SH3 Domain in complex with Choline Kinase fragment 60-69

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Molecular basis for the interaction between human choline kinase alpha and the SH3 domain of the c-Src tyrosine kinase.

Kall, S.L., Whitlatch, K., Smithgall, T.E., Lavie, A.

(2019) Sci Rep 9: 17121-17121

  • DOI: 10.1038/s41598-019-53447-0
  • Primary Citation of Related Structures:  
    6C4S

  • PubMed Abstract: 

    • Choline kinase alpha is a 457-residue protein that catalyzes the reaction between ATP and choline to yield ADP and phosphocholine. This metabolic action has been well studied because of choline kinase's link to cancer malignancy and poor patient prognosis ...

    Choline kinase alpha is a 457-residue protein that catalyzes the reaction between ATP and choline to yield ADP and phosphocholine. This metabolic action has been well studied because of choline kinase's link to cancer malignancy and poor patient prognosis. As the myriad of x-ray crystal structures available for this enzyme show, chemotherapeutic drug design has centered on stopping the catalytic activity of choline kinase and reducing the downstream metabolites it produces. Furthermore, these crystal structures only reveal the catalytic domain of the protein, residues 80-457. However, recent studies provide evidence for a non-catalytic protein-binding role for choline kinase alpha. Here, we show that choline kinase alpha interacts with the SH3 domain of c-Src. Co-precipitation assays, surface plasmon resonance, and crystallographic analysis of a 1.5 Å structure demonstrate that this interaction is specific and is mediated by the poly-proline region found N-terminal to the catalytic domain of choline kinase. Taken together, these data offer strong evidence that choline kinase alpha has a heretofore underappreciated role in protein-protein interactions, which offers an exciting new way to approach drug development against this cancer-enhancing protein.

    Organizational Affiliation: 

    The Jesse Brown VA Medical Center, Chicago, Illinois, 60612, USA. Lavie@uic.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src,cSrc SH3 DomainA, B74Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12931
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.117α = 90
b = 38.753β = 95.7
c = 57.966γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-01-12 
  • Released Date: 2019-01-23 
    • Deposition Author(s): Kall, S.L., Lavie, A.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United States5T32DE018381-10

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-12-04
    Changes: Database references
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence