1SHA | pdb_00001sha

CRYSTAL STRUCTURE OF THE PHOSPHOTYROSINE RECOGNITION DOMAIN SH2 OF V-SRC COMPLEXED WITH TYROSINE-PHOSPHORYLATED PEPTIDES

• PDB DOI: https://doi.org/10.2210/pdb1SHA/pdb

• Classification: PHOSPHOTRANSFERASE
• Organism(s): Rous sarcoma virus
• Mutation(s): No 


• Deposited: 1992-08-18 Released: 1993-10-31 
• Deposition Author(s): Waksman, G., Kuriyan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work: 
  0.208 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal structure of the phosphotyrosine recognition domain SH2 of v-src complexed with tyrosine-phosphorylated peptides.

Waksman, G., Kominos, D., Robertson, S.C., Pant, N., Baltimore, D., Birge, R.B., Cowburn, D., Hanafusa, H., Mayer, B.J., Overduin, M., Resh, M.D., Rios, C.B., Silverman, L., Kuriyan, J.

(1992) Nature 358: 646-653

• PubMed: 1379696 
• DOI: https://doi.org/10.1038/358646a0
• Primary Citation Related Structures: 
  1SHA, 1SHB


• PubMed Abstract: 
  

  Three-dimensional structures of complexes of the SH2 domain of the v-src oncogene product with two phosphotyrosyl peptides have been determined by X-ray crystallography at resolutions of 1.5 and 2.0 A, respectively. A central antiparallel beta-sheet in the structure is flanked by two alpha-helices, with peptide binding mediated by the sheet, intervening loops and one of the helices. The specific recognition of phosphotyrosine involves amino-aromatic interactions between lysine and arginine side chains and the ring system in addition to hydrogen-bonding interactions with the phosphate.

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Organizational Affiliation: 
• Rockefeller University, New York.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.67 kDa 
• Atom Count: 939 
• Modeled Residue Count: 108 
• Deposited Residue Count: 109 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-SRC SH2 DOMAIN	A	104	Rous sarcoma virus	Mutation(s): 0  EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt
Find proteins for P00524 (Rous sarcoma virus subgroup A (strain Schmidt-Ruppin)) Explore P00524  Go to UniProtKB:  P00524

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOPEPTIDE A	B	5	Rous sarcoma virus	Mutation(s): 0  EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P09619 (Homo sapiens) Explore P09619  Go to UniProtKB:  P09619
PHAROS:  P09619 GTEx:  ENSG00000113721

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work:  0.208 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.3	α = 90
b = 57.5	β = 90
c = 39.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Waksman, G., Kuriyan, J.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-30
  Changes: Structure summary