+Open data
-Basic information
Entry | Database: PDB / ID: 7myn | ||||||||||||||||||||||||||||||||||||||||||
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Title | Cryo-EM Structure of p110alpha in complex with p85alpha | ||||||||||||||||||||||||||||||||||||||||||
Components |
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Keywords | TRANSFERASE / phosphoinositide 3-kinase (PI3K) / activation / inhibition / activity-dependent conformational changes | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information perinuclear endoplasmic reticulum membrane / response to muscle inactivity / regulation of toll-like receptor 4 signaling pathway / negative regulation of actin filament depolymerization / phosphatidylinositol kinase activity / response to L-leucine / regulation of actin filament organization / response to butyrate / phosphatidylinositol 3-kinase regulator activity / IRS-mediated signalling ...perinuclear endoplasmic reticulum membrane / response to muscle inactivity / regulation of toll-like receptor 4 signaling pathway / negative regulation of actin filament depolymerization / phosphatidylinositol kinase activity / response to L-leucine / regulation of actin filament organization / response to butyrate / phosphatidylinositol 3-kinase regulator activity / IRS-mediated signalling / positive regulation of focal adhesion disassembly / cellular response to hydrostatic pressure / phosphatidylinositol 3-kinase activator activity / autosome genomic imprinting / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / myeloid leukocyte migration / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / positive regulation of endoplasmic reticulum unfolded protein response / positive regulation of protein localization to membrane / Activated NTRK3 signals through PI3K / negative regulation of fibroblast apoptotic process / cis-Golgi network / ErbB-3 class receptor binding / phosphatidylinositol 3-kinase complex, class IB / kinase activator activity / vasculature development / transmembrane receptor protein tyrosine kinase adaptor activity / regulation of cellular respiration / RHOF GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / RHOD GTPase cycle / cardiac muscle cell contraction / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / enzyme-substrate adaptor activity / Nephrin family interactions / anoikis / relaxation of cardiac muscle / Signaling by LTK in cancer / positive regulation of leukocyte migration / Costimulation by the CD28 family / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / RND1 GTPase cycle / Signaling by LTK / MET activates PI3K/AKT signaling / phosphatidylinositol-4,5-bisphosphate 3-kinase / PI3K/AKT activation / RND2 GTPase cycle / positive regulation of filopodium assembly / RND3 GTPase cycle / phosphatidylinositol 3-kinase / growth hormone receptor signaling pathway / vascular endothelial growth factor signaling pathway / negative regulation of stress fiber assembly / RHOB GTPase cycle / insulin binding / phosphatidylinositol-3-phosphate biosynthetic process / natural killer cell mediated cytotoxicity / 1-phosphatidylinositol-3-kinase activity / RHOV GTPase cycle / negative regulation of cell-matrix adhesion / Signaling by ALK / negative regulation of macroautophagy / GP1b-IX-V activation signalling / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / protein kinase activator activity / PI-3K cascade:FGFR4 / response to dexamethasone / PI-3K cascade:FGFR1 / RHOC GTPase cycle / intracellular glucose homeostasis / RHOJ GTPase cycle / negative regulation of osteoclast differentiation / phosphatidylinositol-mediated signaling / Synthesis of PIPs at the plasma membrane / CD28 dependent PI3K/Akt signaling / phosphatidylinositol phosphate biosynthetic process / RHOU GTPase cycle / CDC42 GTPase cycle / T cell differentiation / PI3K events in ERBB2 signaling / PI3K Cascade / negative regulation of anoikis / intercalated disc / RET signaling / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / extrinsic apoptotic signaling pathway via death domain receptors / RHOG GTPase cycle / regulation of multicellular organism growth / positive regulation of TOR signaling / endothelial cell migration / RHOA GTPase cycle Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å | ||||||||||||||||||||||||||||||||||||||||||
Authors | Liu, X. / Yang, S. / Hart, J.R. / Xu, Y. / Zou, X. / Zhang, H. / Zhou, Q. / Xia, T. / Zhang, Y. / Yang, D. ...Liu, X. / Yang, S. / Hart, J.R. / Xu, Y. / Zou, X. / Zhang, H. / Zhou, Q. / Xia, T. / Zhang, Y. / Yang, D. / Wang, M.-W. / Vogt, P.K. | ||||||||||||||||||||||||||||||||||||||||||
Funding support | United States, China, 13items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Cryo-EM structures of PI3Kα reveal conformational changes during inhibition and activation. Authors: Xiao Liu / Su Yang / Jonathan R Hart / Yingna Xu / Xinyu Zou / Huibing Zhang / Qingtong Zhou / Tian Xia / Yan Zhang / Dehua Yang / Ming-Wei Wang / Peter K Vogt / Abstract: Phosphoinositide 3-kinases (PI3Ks) are lipid kinases essential for growth and metabolism. Their aberrant activation is associated with many types of cancers. Here we used single-particle cryoelectron ...Phosphoinositide 3-kinases (PI3Ks) are lipid kinases essential for growth and metabolism. Their aberrant activation is associated with many types of cancers. Here we used single-particle cryoelectron microscopy (cryo-EM) to determine three distinct conformations of full-length PI3Kα (p110α-p85α): the unliganded heterodimer PI3Kα, PI3Kα bound to the p110α-specific inhibitor BYL-719, and PI3Kα exposed to an activating phosphopeptide. The cryo-EM structures of unbound and of BYL-719-bound PI3Kα are in general accord with published crystal structures. Local deviations are presented and discussed. BYL-719 stabilizes the structure of PI3Kα, but three regions of low-resolution extra density remain and are provisionally assigned to the cSH2, BH, and SH3 domains of p85. One of the extra density regions is in contact with the kinase domain blocking access to the catalytic site. This conformational change indicates that the effects of BYL-719 on PI3Kα activity extend beyond competition with adenosine triphosphate (ATP). In unliganded PI3Kα, the DFG motif occurs in the "in" and "out" positions. In BYL-719-bound PI3Kα, only the DFG-in position, corresponding to the active conformation of the kinase, was observed. The phosphopeptide-bound structure of PI3Kα is composed of a stable core resolved at 3.8 Å. It contains all p110α domains except the adaptor-binding domain (ABD). The p85α domains, linked to the core through the ABD, are no longer resolved, implying that the phosphopeptide activates PI3Kα by fully releasing the niSH2 domain from binding to p110α. The structures presented here show the basal form of the full-length PI3Kα dimer and document conformational changes related to the activated and inhibited states. | ||||||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7myn.cif.gz | 261.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7myn.ent.gz | 192.1 KB | Display | PDB format |
PDBx/mmJSON format | 7myn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7myn_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7myn_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7myn_validation.xml.gz | 143.2 KB | Display | |
Data in CIF | 7myn_validation.cif.gz | 291.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/7myn ftp://data.pdbj.org/pub/pdb/validation_reports/my/7myn | HTTPS FTP |
-Related structure data
Related structure data | 24081MC 7myoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 127822.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CA / Plasmid: pFastBac Dual Details (production host): Baculovirus produces both PIK3CA and PIK3R1 simultaneously Cell (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P42336, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 83623.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Plasmid: pFastBac Dual Details (production host): Baculovirus produces both PIK3CA and PIK3R1 simultaneously Cell (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P27986 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Heterodimer of PIK3CA with PIK3R1 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.2 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) / Cellular location: Membrane associated |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) / Cell: BTI-TN-5B1-4 / Plasmid: pFastBac Dual |
Buffer solution | pH: 7.6 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GRAPHENE OXIDE / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 46685 X / Calibrated defocus min: -1500 nm / Calibrated defocus max: -2500 nm |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4023 |
Image scans | Width: 5760 / Height: 4092 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||
Particle selection | Num. of particles selected: 332105 | |||||||||||||||||||||||||
3D reconstruction | Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 332105 / Symmetry type: POINT | |||||||||||||||||||||||||
Atomic model building | B value: 98.68 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | |||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.31 Å2 | |||||||||||||||||||||||||
Refine LS restraints |
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