3S9K

Crystal structure of the Itk SH2 domain.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.354 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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 68: 145-153

  • DOI: 10.1107/S1744309111049761

  • 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 ...

    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.


    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 67: 269


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ITK/TSK
A
118Mus musculusMutation(s): 0 
Gene Names: Itk (Emt, Tlk, Tsk)
EC: 2.7.10.2
Find proteins for Q03526 (Mus musculus)
Go to UniProtKB:  Q03526
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.354 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.233 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 53.640α = 90.00
b = 57.360β = 90.00
c = 83.190γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SOLVEphasing
d*TREKdata scaling
CrystalCleardata collection
d*TREKdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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