2IUH

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

• PDB DOI: https://doi.org/10.2210/pdb2IUH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• 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: 2.00 Å
• R-Value Free: 0.245 
• R-Value Work: 0.154 
• R-Value Observed: 0.154 

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 PISA (software)

Macromolecule Content

• Total Structure Weight: 15.31 kDa 
• Atom Count: 1,119 
• Modelled Residue Count: 123 
• Deposited Residue Count: 131 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT	A	120	Homo sapiens	Mutation(s): 0
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
C-KIT PHOSPHOTYROSYL PEPTIDE	B	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens) Explore P10721  Go to UniProtKB:  P10721
PHAROS:  P10721 GTEx:  ENSG00000157404

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: 2.00 Å
• R-Value Free: 0.245 
• R-Value Work: 0.154 
• R-Value Observed: 0.154 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.95	α = 90
b = 56.95	β = 90
c = 68.17	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: 2015-10-28
  Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2021-04-28
  Changes: Data collection, Derived calculations