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- PDB-7pg5: Crystal Structure of PI3Kalpha -

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Basic information

Entry
Database: PDB / ID: 7pg5
TitleCrystal Structure of PI3Kalpha
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
KeywordsTRANSFERASE / 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 / positive regulation of focal adhesion disassembly ...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 / positive regulation of focal adhesion disassembly / autosome genomic imprinting / 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 / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / positive regulation of protein localization to membrane / Activated NTRK3 signals through PI3K / cis-Golgi network / ErbB-3 class receptor binding / negative regulation of fibroblast apoptotic process / cardiac muscle cell contraction / RHOF GTPase cycle / kinase activator activity / phosphatidylinositol 3-kinase complex, class IB / vasculature development / transmembrane receptor protein tyrosine kinase adaptor activity / RHOD GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / regulation of cellular respiration / positive regulation of endoplasmic reticulum unfolded protein response / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex, class IA / anoikis / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle / Costimulation by the CD28 family / relaxation of cardiac muscle / positive regulation of leukocyte migration / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / MET activates PI3K/AKT signaling / RND2 GTPase cycle / PI3K/AKT activation / positive regulation of filopodium assembly / RND3 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / vascular endothelial growth factor signaling pathway / negative regulation of stress fiber assembly / growth hormone receptor signaling pathway / phosphatidylinositol 3-kinase / insulin binding / phosphatidylinositol-3-phosphate biosynthetic process / RHOV GTPase cycle / 1-phosphatidylinositol-3-kinase activity / negative regulation of cell-matrix adhesion / Signaling by ALK / RHOB GTPase cycle / negative regulation of macroautophagy / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR2 / response to dexamethasone / RHOJ GTPase cycle / PI-3K cascade:FGFR4 / protein kinase activator activity / 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-mediated signaling / phosphatidylinositol phosphate biosynthetic process / CDC42 GTPase cycle / RHOU GTPase cycle / PI3K events in ERBB2 signaling / negative regulation of anoikis / T cell differentiation / RET signaling / intercalated disc / regulation of multicellular organism growth / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / RHOG GTPase cycle / extrinsic apoptotic signaling pathway via death domain receptors / PI3K Cascade / RHOA GTPase cycle / positive regulation of TOR signaling / endothelial cell migration / RAC2 GTPase cycle / RAC3 GTPase cycle / Role of phospholipids in phagocytosis
Similarity search - Function
PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain ...PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Rho GTPase activation protein / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Phosphatidylinositol 3-kinase regulatory subunit alpha / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20029074868 Å
AuthorsGong, G. / Pinotsis, N. / Williams, R.L. / Vanhaesebroeck, B.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: 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
DepositionAug 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,0965
Polymers158,8142
Non-polymers2823
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-32 kcal/mol
Surface area57620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.4251, 105.2443, 136.0864
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform / PI3-kinase subunit alpha / PI3K-alpha / PI3Kalpha / PtdIns-3-kinase subunit alpha / ...PI3-kinase subunit alpha / PI3K-alpha / PI3Kalpha / PtdIns-3-kinase subunit alpha / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit alpha / PtdIns-3-kinase subunit p110-alpha / p110alpha / Phosphoinositide 3-kinase alpha / Phosphoinositide-3-kinase catalytic alpha polypeptide / Serine/threonine protein kinase PIK3CA


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
#2: Protein Phosphatidylinositol 3-kinase regulatory subunit alpha / PI3-kinase regulatory subunit alpha / PI3K regulatory subunit alpha / PtdIns-3-kinase regulatory ...PI3-kinase regulatory subunit alpha / PI3K regulatory subunit alpha / PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha / PI3-kinase subunit p85-alpha / PtdIns-3-kinase regulatory subunit p85-alpha


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 ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.2→2.25 Å / Redundancy: 5.3 % / Num. unique obs: 4522 / CC1/2: 0.398 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JPS

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
RfactorNum. reflection% reflection
Rfree0.24560820669 3983 5.14892186773 %
Rwork0.19642042793 73373 -
obs0.198998535605 77356 99.9470263705 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.2856298507 Å2
Refinement stepCycle: LAST / Resolution: 2.20029074868→57.1698004554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10581 0 16 152 10749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087903340130110863
X-RAY DIFFRACTIONf_angle_d1.1448159305314672
X-RAY DIFFRACTIONf_chiral_restr0.04322192189161591
X-RAY DIFFRACTIONf_plane_restr0.005536393493161888
X-RAY DIFFRACTIONf_dihedral_angle_d15.92620160424147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.22710.3330214756651470.2782228078222544X-RAY DIFFRACTION99.2988929889
2.2271-2.25530.3231181949931500.2757905289382579X-RAY DIFFRACTION99.7077091706
2.2553-2.2850.2952613018721350.2780261577612590X-RAY DIFFRACTION100
2.285-2.31630.3237643998251300.2694449527592594X-RAY DIFFRACTION100
2.3163-2.34940.3104581017641510.2555776887262592X-RAY DIFFRACTION100
2.3494-2.38450.2825602192291600.2398254573192591X-RAY DIFFRACTION100
2.3845-2.42170.3013846044471240.2410999006632574X-RAY DIFFRACTION99.9629492405
2.4217-2.46140.2647401267941330.2349798761112645X-RAY DIFFRACTION100
2.4614-2.50390.3097204155741450.2381022350772567X-RAY DIFFRACTION100
2.5039-2.54940.2748751787861360.2412066188492572X-RAY DIFFRACTION100
2.5494-2.59840.3255055139191200.2342363147822615X-RAY DIFFRACTION99.9634502924
2.5984-2.65150.2969821630611070.2305045667312663X-RAY DIFFRACTION99.9639119451
2.6515-2.70910.3071945374311350.2367102358352622X-RAY DIFFRACTION100
2.7091-2.77210.2940392886711430.2317338970972634X-RAY DIFFRACTION100
2.7721-2.84150.299392976631440.240253490452568X-RAY DIFFRACTION100
2.8415-2.91830.3005191828951560.2344002767742616X-RAY DIFFRACTION100
2.9183-3.00420.3076510182361530.2347315496872572X-RAY DIFFRACTION99.9633162142
3.0042-3.10110.2756470262321180.2459524035232679X-RAY DIFFRACTION100
3.1011-3.21190.3096114781241530.2328868156152556X-RAY DIFFRACTION100
3.2119-3.34050.2665106503791490.2203140581522610X-RAY DIFFRACTION100
3.3405-3.49250.2789867646221510.2142458498722636X-RAY DIFFRACTION100
3.4925-3.67660.2438001279561380.2024444931472650X-RAY DIFFRACTION100
3.6766-3.9070.2274809788311560.1880565482492615X-RAY DIFFRACTION100
3.907-4.20850.2469089771721390.1721251607512658X-RAY DIFFRACTION100
4.2085-4.63190.1901040953271640.1543543172752633X-RAY DIFFRACTION99.9642601858
4.6319-5.30170.2117059528631720.153066260612637X-RAY DIFFRACTION100
5.3017-6.6780.2279974842571390.191528189492717X-RAY DIFFRACTION100
6.678-100.1708091326871350.1495952460522844X-RAY DIFFRACTION99.6987951807
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.528910015860.7632470370520.4346737714910.6016662949980.312412332470.907897808685-0.104997687802-0.003899470517010.08593867423960.1054048412370.12990718114-0.41183827867-0.09787578049280.512144862512-0.03846866015290.4128850848670.05002774102890.0006873408377080.316392283793-0.003994454596240.30734444578317.8138755248-36.393400678438.3437724799
22.08989526181-0.290160492646-0.2107411210831.849871901120.1410424539822.65785106693-0.004004882651330.701724748181-0.433758960354-0.585644274929-0.0295931589040.08988601350360.467419744925-0.2653074589630.04263624021430.476997835651-0.05377018085020.004696451147050.593394320079-0.1364917798230.394867912933-4.5714192294-38.2682943491.79873287695
31.45702945512-0.3957735403740.05214413492461.012834915140.03919786941391.5200691741-0.04779714402990.03243195742380.0851508005260.04097704630620.01166644167770.170926155565-0.0349599964192-0.2319787658930.01887959726840.27724463173-0.02240039453130.008897612776660.255169253024-0.01705555173810.314919023444-16.8985222525-21.986729785230.2900748079
41.3395868017-0.518208274925-0.1919585151471.90605842346-0.2088923308421.52964642299-0.0380346162570.01316260209010.06202146768980.492583244421-0.04160946168441.07559953214-0.172925879612-0.6060563067790.04300270514320.7987218507190.252534736240.1651908070890.997046868201-0.05436466394631.01269910536-46.3525220953-13.465071937944.5518105526
52.55749805597-1.41527494033-0.1918278241171.73455967419-0.0890695999320.678548429875-0.20164611587-0.3271146413860.2497111671160.2861165140350.267540033742-0.131746963268-0.04303081278290.0462804222553-0.02628624569420.559905053773-0.00671027683526-0.006139765725650.474451934591-0.05264130002010.4500905457534.84566686876-16.172237744651.7262813196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 3:160))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 161:313))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 322:1065))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 326:439))
5X-RAY DIFFRACTION5chain 'B' and ((resseq 440:591))

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