4OVU

Crystal Structure of p110alpha in complex with niSH2 of p85alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of nSH2 regulation and lipid binding in PI3K alpha.

Miller, M.S.Schmidt-Kittler, O.Bolduc, D.M.Brower, E.T.Chaves-Moreira, D.Allaire, M.Kinzler, K.W.Jennings, I.G.Thompson, P.E.Cole, P.A.Amzel, L.M.Vogelstein, B.Gabelli, S.B.

(2014) Oncotarget 5: 5198-5208

  • DOI: https://doi.org/10.18632/oncotarget.2263
  • Primary Citation of Related Structures:  
    4OVU, 4OVV

  • PubMed Abstract: 

    We report two crystal structures of the wild-type phosphatidylinositol 3-kinase α (PI3Kα) heterodimer refined to 2.9 Å and 3.4 Å resolution: the first as the free enzyme, the second in complex with the lipid substrate, diC4-PIP₂, respectively. The first structure shows key interactions of the N-terminal SH2 domain (nSH2) and iSH2 with the activation loop that suggest a mechanism by which the enzyme is inhibited in its basal state. In the second structure, the lipid substrate binds in a positively charged pocket adjacent to the ATP-binding site, bordered by the P-loop, the activation loop and the iSH2 domain. An additional lipid-binding site was identified at the interface of the ABD, iSH2 and kinase domains. The ability of PI3Kα to bind an additional PIP₂ molecule was confirmed in vitro by fluorescence quenching experiments. The crystal structures reveal key differences in the way the nSH2 domain interacts with wild-type p110α and with the oncogenic mutant p110αH1047R. Increased buried surface area and two unique salt-bridges observed only in the wild-type structure suggest tighter inhibition in the wild-type PI3Kα than in the oncogenic mutant. These differences may be partially responsible for the increased basal lipid kinase activity and increased membrane binding of the oncogenic mutant.


  • Organizational Affiliation

    Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia. Present Address: Department of Oncology, Johns Hopkins University School of Medicine, Baltimore Maryland, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform1,096Homo sapiensMutation(s): 0 
Gene Names: PIK3CA
EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens)
Explore P42336 
Go to UniProtKB:  P42336
PHAROS:  P42336
GTEx:  ENSG00000121879 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42336
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alpha279Homo sapiensMutation(s): 0 
Gene Names: GRB1PI3KR1PIK3R1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens)
Explore P27986 
Go to UniProtKB:  P27986
PHAROS:  P27986
GTEx:  ENSG00000145675 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27986
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.692α = 90
b = 116.205β = 90
c = 149.086γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR37 CA043460

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description