+Open data
-Basic information
Entry | Database: PDB / ID: 7pg5 | |||||||||
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Title | Crystal Structure of PI3Kalpha | |||||||||
Components |
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Keywords | TRANSFERASE / PI3K / PIK3CA / PIK3R1 / p110 / p85 / compound | |||||||||
Function / homology | Function and homology information perinuclear endoplasmic reticulum membrane / response to muscle inactivity / negative regulation of actin filament depolymerization / regulation of toll-like receptor 4 signaling pathway / response to L-leucine / phosphatidylinositol kinase activity / regulation of actin filament organization / phosphatidylinositol 3-kinase regulator activity / response to butyrate / autosome genomic imprinting ...perinuclear endoplasmic reticulum membrane / response to muscle inactivity / negative regulation of actin filament depolymerization / regulation of toll-like receptor 4 signaling pathway / response to L-leucine / phosphatidylinositol kinase activity / regulation of actin filament organization / phosphatidylinositol 3-kinase regulator activity / response to butyrate / autosome genomic imprinting / positive regulation of focal adhesion disassembly / IRS-mediated signalling / cellular response to hydrostatic pressure / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / myeloid leukocyte migration / phosphatidylinositol 3-kinase regulatory subunit binding / 1-phosphatidylinositol-3-kinase regulator activity / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / positive regulation of protein localization to membrane / cis-Golgi network / Activated NTRK3 signals through PI3K / kinase activator activity / ErbB-3 class receptor binding / negative regulation of fibroblast apoptotic process / RHOF GTPase cycle / cardiac muscle cell contraction / phosphatidylinositol 3-kinase complex, class IB / vasculature development / transmembrane receptor protein tyrosine kinase adaptor activity / RHOD GTPase cycle / positive regulation of endoplasmic reticulum unfolded protein response / Signaling by cytosolic FGFR1 fusion mutants / regulation of cellular respiration / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex / anoikis / Nephrin family interactions / 1-phosphatidylinositol-4-phosphate 3-kinase activity / RND1 GTPase cycle / Costimulation by the CD28 family / vascular endothelial growth factor signaling pathway / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / RND2 GTPase cycle / MET activates PI3K/AKT signaling / PI3K/AKT activation / RND3 GTPase cycle / positive regulation of leukocyte migration / phosphatidylinositol-4,5-bisphosphate 3-kinase / positive regulation of filopodium assembly / phosphatidylinositol 3-kinase complex, class IA / negative regulation of stress fiber assembly / phosphatidylinositol 3-kinase / relaxation of cardiac muscle / growth hormone receptor signaling pathway / phosphatidylinositol-3-phosphate biosynthetic process / insulin binding / 1-phosphatidylinositol-3-kinase activity / RHOV GTPase cycle / negative regulation of macroautophagy / RHOB GTPase cycle / Signaling by ALK / negative regulation of cell-matrix adhesion / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / protein kinase activator activity / response to dexamethasone / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / RHOJ GTPase cycle / RHOC GTPase cycle / PI-3K cascade:FGFR1 / negative regulation of osteoclast differentiation / intracellular glucose homeostasis / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / CDC42 GTPase cycle / RHOU GTPase cycle / PI3K events in ERBB2 signaling / Signaling by ALK fusions and activated point mutants / RHOG GTPase cycle / negative regulation of anoikis / RET signaling / T cell differentiation / regulation of multicellular organism growth / extrinsic apoptotic signaling pathway via death domain receptors / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / intercalated disc / RHOA GTPase cycle / positive regulation of TOR signaling / endothelial cell migration / RAC2 GTPase cycle / RAC3 GTPase cycle / GAB1 signalosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20029074868 Å | |||||||||
Authors | Gong, G. / Pinotsis, N. / Williams, R.L. / Vanhaesebroeck, B. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nature / Year: 2023 Title: A small-molecule PI3K alpha activator for cardioprotection and neuroregeneration. Authors: Gong, G.Q. / Bilanges, B. / Allsop, B. / Masson, G.R. / Roberton, V. / Askwith, T. / Oxenford, S. / Madsen, R.R. / Conduit, S.E. / Bellini, D. / Fitzek, M. / Collier, M. / Najam, O. / He, Z. ...Authors: Gong, G.Q. / Bilanges, B. / Allsop, B. / Masson, G.R. / Roberton, V. / Askwith, T. / Oxenford, S. / Madsen, R.R. / Conduit, S.E. / Bellini, D. / Fitzek, M. / Collier, M. / Najam, O. / He, Z. / Wahab, B. / McLaughlin, S.H. / Chan, A.W.E. / Feierberg, I. / Madin, A. / Morelli, D. / Bhamra, A. / Vinciauskaite, V. / Anderson, K.E. / Surinova, S. / Pinotsis, N. / Lopez-Guadamillas, E. / Wilcox, M. / Hooper, A. / Patel, C. / Whitehead, M.A. / Bunney, T.D. / Stephens, L.R. / Hawkins, P.T. / Katan, M. / Yellon, D.M. / Davidson, S.M. / Smith, D.M. / Phillips, J.B. / Angell, R. / Williams, R.L. / Vanhaesebroeck, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pg5.cif.gz | 655.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pg5.ent.gz | 448.9 KB | Display | PDB format |
PDBx/mmJSON format | 7pg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/7pg5 ftp://data.pdbj.org/pub/pdb/validation_reports/pg/7pg5 | HTTPS FTP |
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-Related structure data
Related structure data | 7pg6C 8bfuC 8ow2C 4jpsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 124458.984 Da / Num. of mol.: 1 / Mutation: M232K, L233K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CA / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P42336, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase | ||||||
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#2: Protein | Mass: 34354.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27986 | ||||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.25 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 10% PEG 5K MME (w/v), 160 nM KSCN, 100 mM sodium cacodylate pH 6.5. PH range: 6-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→136.09 Å / Num. obs: 77356 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 54.84 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.08 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 5.3 % / Num. unique obs: 4522 / CC1/2: 0.398 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JPS Resolution: 2.20029074868→57.1698004554 Å / SU ML: 0.308552115365 / Cross valid method: FREE R-VALUE / σ(F): 1.33790043936 / Phase error: 27.0368633453
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.2856298507 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.20029074868→57.1698004554 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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