4ZNX

Crystal structure of the Fyn-SH3 domain in complex with the high affinity peptide APP12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase.

Camara-Artigas, A.Ortiz-Salmeron, E.Andujar-Sanchez, M.Bacarizo, J.Martin-Garcia, J.M.

(2016) Acta Crystallogr.,Sect.F 72: 707-712

  • DOI: 10.1107/S2053230X16012310

  • PubMed Abstract: 
  • Interactions of proline-rich motifs with SH3 domains are present in signal transduction and other important cell processes. Analysis of structural and thermodynamic data suggest a relevant role of water molecules in these protein-protein interactions ...

    Interactions of proline-rich motifs with SH3 domains are present in signal transduction and other important cell processes. Analysis of structural and thermodynamic data suggest a relevant role of water molecules in these protein-protein interactions. To determine whether or not the SH3 domain of the Fyn tyrosine kinase shows the same behaviour, the crystal structures of its complexes with two high-affinity synthetic peptides, VSL12 and APP12, which are class I and II peptides, respectively, have been solved. In the class I complexes two water molecules were found at the binding interface that were not present in the class II complexes. The structures suggest a role of these water molecules in facilitating conformational changes in the SH3 domain to allow the binding of the class I or II peptides. In the third binding pocket these changes modify the cation-π and salt-bridge interactions that determine the affinity of the binding. Comparison of the water molecules involved in the binding of the peptides with previous reported hydration spots suggests a different pattern for the SH3 domains of the Src tyrosine kinase family.


    Organizational Affiliation

    Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento, 04120 Almeria, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase Fyn
A, B, C, D
58Homo sapiensMutation(s): 0 
Gene Names: FYN
EC: 2.7.10.2
Find proteins for P06241 (Homo sapiens)
Go to Gene View: FYN
Go to UniProtKB:  P06241
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
APP12
E, F, G, H
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 31.658α = 90.00
b = 76.664β = 94.74
c = 73.175γ = 90.00
Software Package:
Software NamePurpose
AutoPROCdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
AutoPROCdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-05-05 
  • Released Date: 2016-06-29 
  • Deposition Author(s): Camara-Artigas, A.

Funding OrganizationLocationGrant Number
MINECOSpainBIO2012-39922-C02-02

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2016-09-28
    Type: Database references