6F3F

Autoinhibited Src kinase bound to ADP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41796 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

A switch in nucleotide affinity governs activation of the Src and Tec family kinases.

von Raussendorf, F., de Ruiter, A., Leonard, T.A.

(2017) Sci Rep 7: 17405-17405

  • DOI: 10.1038/s41598-017-17703-5

  • PubMed Abstract: 

    • The Tec kinases, closely related to Src family kinases, are essential for lymphocyte function in the adaptive immune system. Whilst the Src and Abl kinases are regulated by tail phosphorylation and N-terminal myristoylation respectively, the Tec kina ...

    The Tec kinases, closely related to Src family kinases, are essential for lymphocyte function in the adaptive immune system. Whilst the Src and Abl kinases are regulated by tail phosphorylation and N-terminal myristoylation respectively, the Tec kinases are notable for the absence of either regulatory element. We have found that the inactive conformations of the Tec kinase Itk and Src preferentially bind ADP over ATP, stabilising both proteins. We demonstrate that Itk adopts the same conformation as Src and that the autoinhibited conformation of Src is independent of its C-terminal tail. Allosteric activation of both Itk and Src depends critically on the disruption of a conserved hydrophobic stack that accompanies regulatory domain displacement. We show that a conformational switch permits the exchange of ADP for ATP, leading to efficient autophosphorylation and full activation. In summary, we propose a universal mechanism for the activation and autoinhibition of the Src and Tec kinases.

    Organizational Affiliation: 

    Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria.,Department of Medical Biochemistry, Medical University of Vienna, 1090, Vienna, Austria. thomas.leonard@meduniwien.ac.at.,Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Campus Vienna Biocenter 5, 1030, Vienna, Austria.,Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Campus Vienna Biocenter 5, 1030, Vienna, Austria. thomas.leonard@meduniwien.ac.at.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase
A
455Mus musculusMutation(s): 0 
Gene Names: Src
EC: 2.7.10.2
Find proteins for P05480 (Mus musculus)
Go to UniProtKB:  P05480
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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: 2.41796 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.011α = 90.00
b = 82.974β = 90.00
c = 105.051γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP28135

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release