Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.73 kDa 
• Atom Count: 960 
• Residue Count: 114 
• Unique protein chains: 1

3S9K

Crystal structure of the Itk SH2 domain.

• DOI: 10.2210/pdb3S9K/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-06-01 Released: 2012-02-08 
• Deposition Author(s): Joseph, R.E., Ginder, N.D., Hoy, J.A., Nix, J.C., Fulton, B.D., Honzatko, R.B., Andreotti, A.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.283 
• R-Value Work: 0.233 
• R-Value Observed: 0.237 

Literature

Structure of the interleukin-2 tyrosine kinase Src homology 2 domain; comparison between X-ray and NMR-derived structures.

Joseph, R.E., Ginder, N.D., Hoy, J.A., Nix, J.C., Fulton, D.B., Honzatko, R.B., Andreotti, A.H.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 145-153

• PubMed: 22297986 
• DOI: 10.1107/S1744309111049761
• Primary Citation of Related Structures:  
  3S9K


• PubMed Abstract: 
  

The crystal structure of the interleukin-2 tyrosine kinase Src homology domain (Itk SH2) is described and it is found that unlike in studies of this domain using NMR spectroscopy, cis-trans-prolyl isomerization is not readily detected in the crystal structure. Based on similarities between the Itk SH2 crystal form and the cis form of the Itk SH2 NMR structure, it is concluded that it is likely that the prolyl imide bond at least in part adopts the cis conformation in the crystal form. However, the lack of high-resolution data and the dynamic nature of the proline-containing loop mean that the precise imide-bond conformation cannot be determined and prolyl cis-trans isomerization in the crystal cannot be ruled out. Given the preponderance of structures that have been solved by X-ray crystallography in the Protein Data Bank, this result supports the notion that prolyl isomerization in folded proteins has been underestimated among known structures. Interestingly, while the precise status of the proline residue is ambiguous, Itk SH2 crystallizes as a domain-swapped dimer. The domain-swapped structure of Itk SH2 is similar to the domain-swapped SH2 domains of Grb2 and Nck, with domain swapping occurring at the β-meander region of all three SH2 domains. Thus, for Itk SH2 structural analysis by NMR spectroscopy and X-ray crystallography revealed very different structural features: proline isomerization versus domain-swapped dimerization, respectively.

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Related Citations: 

• Purification, crystallization and preliminary crystallographic analysis of the SH2 domain of IL-2-inducible T-cell kinase.
  Joseph, R.E., Ginder, N.D., Hoy, J.A., Nix, J.C., Honzatko, R.B., Andreotti, A.H.
  (2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 269

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Organizational Affiliation: 

Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ITK/TSK	A	118	Mus musculus	Mutation(s): 0  Gene Names: Emt, IL-2 inducible T cell kinase, Itk, Tlk, Tsk EC: 2.7.10.2
Find proteins for Q03526 (Mus musculus) Explore Q03526  Go to UniProtKB:  Q03526

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	A	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.283 
• R-Value Work: 0.233 
• R-Value Observed: 0.237 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.64	α = 90
b = 57.36	β = 90
c = 83.19	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-01 
• Released Date: 2012-02-08 
Deposition Author(s): Joseph, R.E., Ginder, N.D., Hoy, J.A., Nix, J.C., Fulton, B.D., Honzatko, R.B., Andreotti, A.H.

Revision History 

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2012-02-15
  Changes: Database references