4OVV

Crystal Structure of PI3Kalpha in complex with diC4-PIP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.18632/oncotarget.2263
  • Primary Citation of Related Structures:  

  • 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 fi ...

    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.,Photon Sciences, Brookhaven National Laboratory, Upton, New York, USA.,Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institutions, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. Present Address: Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institutions, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. Present Address: Paragon Bioservices, Baltimore, Maryland.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institutions, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. Present Address: Sanofi, Cambridge, Massachusetts. Present Address: Berkeley Center for Structural Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
A
1096Homo sapiensMutation(s): 0 
Gene Names: PIK3CA
EC: 2.7.1.153
Find proteins for P42336 (Homo sapiens)
Go to Gene View: PIK3CA
Go to UniProtKB:  P42336
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alpha
B
279Homo sapiensMutation(s): 0 
Gene Names: PIK3R1 (GRB1)
Find proteins for P27986 (Homo sapiens)
Go to Gene View: PIK3R1
Go to UniProtKB:  P27986
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
PBU
Query on PBU

Download SDF File 
Download CCD File 
A, B
(2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1,2-DIYL DIBUTANOATE
di-butanoyl L-alpha-phosphatidyl-D-myo-inositol 4,5-bisphosphate; di-C4-PIP2
C17 H33 O19 P3
DHAFWWKSHUBGAH-BXJBXBQISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 114.259α = 90.00
b = 116.083β = 90.00
c = 148.743γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR37 CA043460

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Structure summary
  • Version 1.2: 2016-08-24
    Type: Other
  • Version 1.3: 2016-08-31
    Type: Experimental preparation
  • Version 1.4: 2017-09-27
    Type: Author supporting evidence, Derived calculations