2Y3A

Crystal structure of p110beta in complex with icSH2 of p85beta and the drug GDC-0941

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

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This is version 1.3 of the entry. See complete history. 


Literature

Structure of Lipid Kinase P110Beta-P85Beta Elucidates an Unusual Sh2-Domain-Mediated Inhibitory Mechanism.

Zhang, X., Vadas, O., Perisic, O., Anderson, K.E., Clark, J., Hawkins, P.T., Stephens, L.R., Williams, R.L.

(2011) Mol Cell 41: 567

  • DOI: 10.1016/j.molcel.2011.01.026
  • Primary Citation of Related Structures:  
    2Y3A

  • PubMed Abstract: 

    • Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. The structure of a p110β/p85β complex identifies an inhibitory function for the C-terminal SH2 domain (cSH2) of the p85 regulatory subunit. Mutagenesis of a cSH2 c ...

    Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. The structure of a p110β/p85β complex identifies an inhibitory function for the C-terminal SH2 domain (cSH2) of the p85 regulatory subunit. Mutagenesis of a cSH2 contact residue activates downstream signaling in cells. This inhibitory contact ties up the C-terminal region of the p110β catalytic subunit, which is essential for lipid kinase activity. In vitro, p110β basal activity is tightly restrained by contacts with three p85 domains: the cSH2, nSH2, and iSH2. RTK phosphopeptides relieve inhibition by nSH2 and cSH2 using completely different mechanisms. The binding site for the RTK's pYXXM motif is exposed on the cSH2, requiring an extended RTK motif to reach and disrupt the inhibitory contact with p110β. This contrasts with the nSH2 where the pY-binding site itself forms the inhibitory contact. This establishes an unusual mechanism by which p85 SH2 domains contribute to RTK signaling specificities.

    Organizational Affiliation: 

    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT BETA ISOFORM A1092Mus musculusMutation(s): 0 
Gene Names: Pik3cb
EC: 2.7.1.173 (PDB Primary Data), 2.7.1.153 (UniProt)
Find proteins for Q8BTI9 (Mus musculus)
Explore Q8BTI9 
Go to UniProtKB:  Q8BTI9
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT BETA B302Mus musculusMutation(s): 0 
Gene Names: Pik3r2
Find proteins for O08908 (Mus musculus)
Explore O08908 
Go to UniProtKB:  O08908
NIH Common Fund Data Resources
IMPC:  MGI:1098772
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GD9
Query on GD9
Download Ideal Coordinates CCD File 
A
2-(1H-indazol-4-yl)-6-{[4-(methylsulfonyl)piperazin-1-yl]methyl}-4-morpholin-4-yl-thieno[3,2-d]pyrimidine
C23 H27 N7 O3 S2
LHNIIDJUOCFXAP-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.314α = 90
b = 134.314β = 90
c = 428.062γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-16
    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: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy