2Y3A

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 cS ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT BETA ISOFORM
A
1092Mus musculusGene Names: Pik3cb
EC: 2.7.1.153
Find proteins for Q8BTI9 (Mus musculus)
Go to UniProtKB:  Q8BTI9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT BETA
B
302Mus musculusGene Names: Pik3r2
Find proteins for O08908 (Mus musculus)
Go to UniProtKB:  O08908
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GD9
Query on GD9

Download SDF File 
Download 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GD9IC50: 17 - 33 nM (95) BINDINGDB
GD9Kd: 16 nM (95) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.234 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 134.314α = 90.00
b = 134.314β = 90.00
c = 428.062γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
BUSTERrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance