2IUI

Crystal structure of the PI3-kinase p85 N-terminal SH2 domain in complex with PDGFR phosphotyrosyl peptide

• PDB DOI: https://doi.org/10.2210/pdb2IUI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-06-03 Released: 2006-06-06 
• Deposition Author(s): Nolte, R.T., Eck, M.J., Schlessinger, J., Shoelson, S.E., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.248 
• R-Value Work: 0.178 
• R-Value Observed: 0.178 

Literature

Crystal Structure of the Pi 3-Kinase P85 Amino- Terminal Sh2 Domain and its Phosphopeptide Complexes

Nolte, R.T., Eck, M.J., Schlessinger, J., Shoelson, S.E., Harrison, S.C.

(1996) Nat Struct Biol 3: 364

• PubMed: 8599763 
• DOI: https://doi.org/10.1038/nsb0496-364
• Primary Citation of Related Structures:  
  2IUG, 2IUH, 2IUI


• PubMed Abstract: 
  

  Crystal structures of the amino-terminal SH2 domain of the p85alpha subunit of phosphatidylinositol (PI) 3-kinase, alone and in complex with phosphopeptides bearing pTyr-Met/Val-Xaa-Met motifs, show that phosphopeptides bind in the two-pronged manner seen in high-affinity Lck and Src SH2 complexes, with conserved interactions between the domain and the peptide segment from phosphotyrosine to Met+3. Peptide binding requires the rearrangement of a tyrosyl side chain in the BG loop to create the hydrophobic Met+3 binding pocket. The structures suggest a mechanism for the biological specificity exhibited by PI 3-kinase in its interactions with phosphoprotein partners.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Laboratory of Molecular Medicine, Children's Hospital, Boston, Massachusetts 02115, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 30.66 kDa 
• Atom Count: 2,087 
• Modelled Residue Count: 239 
• Deposited Residue Count: 262 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase regulatory subunit alpha	A, B	120	Homo sapiens	Mutation(s): 0  Gene Names: PIK3R1, GRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens) Explore P27986  Go to UniProtKB:  P27986
PHAROS:  P27986 GTEx:  ENSG00000145675

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet-derived growth factor receptor beta	C, D	11	Homo sapiens	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	C, D	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.248 
• R-Value Work: 0.178 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.76	α = 90
b = 61.94	β = 90
c = 108.36	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-06 
Deposition Author(s): Nolte, R.T., Eck, M.J., Schlessinger, J., Shoelson, S.E., Harrison, S.C.

Revision History  

• Version 1.0: 2006-06-06
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2021-04-28
  Changes: Data collection, Derived calculations, Refinement description