Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.15 kDa 
• Atom Count: 945 
• Residue Count: 104 
• Unique protein chains: 1

1F2F

SRC SH2 THREF1TRP MUTANT

• DOI: 10.2210/pdb1F2F/pdb

• Classification: TRANSFERASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-05-24 Released: 2000-07-06 
• Deposition Author(s): Kimber, M.S., Nachman, J., Cunningham, A.M., Gish, G.D., Pawson, T., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.240 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Structural basis for specificity switching of the Src SH2 domain.

Kimber, M.S., Nachman, J., Cunningham, A.M., Gish, G.D., Pawson, T., Pai, E.F.

(2000) Mol Cell 5: 1043-1049

• PubMed: 10911998 
• DOI: 10.1016/s1097-2765(00)80269-5
• Primary Citation of Related Structures:  
  1F1W, 1F2F


• PubMed Abstract: 
  

The Src SH2 domain binds pYEEI-containing phosphopeptides in an extended conformation with a hydrophobic pocket, which includes ThrEF1, binding Ile(pY +3). Mutating ThrEF1 to tryptophan switches specificity to an Asn(pY +2) requirement, yielding a biological mimic of the Grb2 SH2 domain. Here we show that the Src ThrEF1Trp SH2 domain mutant binds pYVNV phosphopeptides in a beta turn conformation, which, despite differing conformations of the interacting tryptophan, closely resembles the native Grb2/pYVNV cognate peptide binding mode. The ThrEF1Trp substitution therefore switches specificity by physically occluding the pTyr +3 binding pocket and by providing additional interaction surface area for Asn(pY +2). This demonstrates structurally how novel SH2 domain specificities may rapidly evolve through single amino acid substitutions and suggests how new signaling pathways may develop.

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Organizational Affiliation: 

Department of Molecular and Medical Genetics, University of Toronto, Ontario, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC	A	104	Gallus gallus	Mutation(s): 1  Gene Names: SRC EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
Find proteins for P00523 (Gallus gallus) Explore P00523  Go to UniProtKB:  P00523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.240 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.46	α = 90
b = 27.22	β = 106.68
c = 55.25	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-05-24 
• Released Date: 2000-07-06 
Deposition Author(s): Kimber, M.S., Nachman, J., Cunningham, A.M., Gish, G.D., Pawson, T., Pai, E.F.

Revision History 

• Version 1.0: 2000-07-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance