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)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 52.49 kDa 
• Atom Count: 3729 
• Modelled Residue Count: 449 
• Deposited Residue Count: 455 
• Unique protein chains: 1

6F3F

Autoinhibited Src kinase bound to ADP

• PDB DOI: 10.2210/pdb6F3F/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-11-28 Released: 2017-12-27 
• Deposition Author(s): von Raussendorf, F., Leonard, T.A.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.268 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

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

• PubMed: 29234112 
• DOI: 10.1038/s41598-017-17703-5
• Primary Citation of Related Structures:  
  6F3F


• 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 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.

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Organizational Affiliation: 

Department of Medical Biochemistry, Medical University of Vienna, 1090, Vienna, Austria. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase	A	455	Mus musculus	Mutation(s): 0  Gene Names: Src EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05480 (Mus musculus) Explore P05480  Go to UniProtKB:  P05480
IMPC:  MGI:98397

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
PTR	BindingDB:  6F3F	-TΔS: -1.81e+1 (kJ/mol) from 1 assay(s)
		ΔG: -2.14e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.268 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.011	α = 90
b = 82.974	β = 90
c = 105.051	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-11-28 
• Released Date: 2017-12-27 
Deposition Author(s): von Raussendorf, F., Leonard, T.A.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P28135

Revision History  

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