4TZI

Structure of unliganded Lyn SH2 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Tyrosine Phosphorylation of the Lyn Src Homology 2 (SH2) Domain Modulates Its Binding Affinity and Specificity.

Jin, L.L.Wybenga-Groot, L.E.Tong, J.Taylor, P.Minden, M.D.Trudel, S.McGlade, C.J.Moran, M.F.

(2015) Mol.Cell Proteomics 14: 695-706

  • DOI: 10.1074/mcp.M114.044404

  • PubMed Abstract: 
  • Src homology 2 (SH2) domains are modular protein structures that bind phosphotyrosine (pY)-containing polypeptides and regulate cellular functions through protein-protein interactions. Proteomics analysis showed that the SH2 domains of Src family kin ...

    Src homology 2 (SH2) domains are modular protein structures that bind phosphotyrosine (pY)-containing polypeptides and regulate cellular functions through protein-protein interactions. Proteomics analysis showed that the SH2 domains of Src family kinases are themselves tyrosine phosphorylated in blood system cancers, including acute myeloid leukemia, chronic lymphocytic leukemia, and multiple myeloma. Using the Src family kinase Lyn SH2 domain as a model, we found that phosphorylation at the conserved SH2 domain residue Y(194) impacts the affinity and specificity of SH2 domain binding to pY-containing peptides and proteins. Analysis of the Lyn SH2 domain crystal structure supports a model wherein phosphorylation of Y(194) on the EF loop modulates the binding pocket that engages amino acid side chains at the pY+2/+3 position. These data indicate another level of regulation wherein SH2-mediated protein-protein interactions are modulated by SH2 kinases and phosphatases.


    Organizational Affiliation

    From the ‡Molecular Structure and Function, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada; ‡‡Departments of Molecular Genetics, Medical Science Building, Room 4386, 1 King's College Circle, Toronto, ON M5S 1A8, Canada;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase Lyn
A, B
115Mus musculusMutation(s): 0 
Gene Names: Lyn
EC: 2.7.10.2
Find proteins for P25911 (Mus musculus)
Go to UniProtKB:  P25911
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.915α = 90.00
b = 27.995β = 96.81
c = 74.915γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHASERphasing
PHENIXrefinement
HKL-3000data collection
Cootmodel building
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-07-10 
  • Released Date: 2015-01-21 
  • Deposition Author(s): Wybenga-Groot, L.E.

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Database references
  • Version 1.2: 2015-04-01
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Derived calculations, Other, Refinement description, Source and taxonomy