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- PDB-2rd0: Structure of a human p110alpha/p85alpha complex -

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Basic information

Entry
Database: PDB / ID: 2rd0
TitleStructure of a human p110alpha/p85alpha complex
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
KeywordsTransferase/Oncoprotein / Disease mutation / Kinase / Oncogene / Transferase / Host-virus interaction / Phosphorylation / SH2 domain / SH3 domain / Transferase-Oncoprotein COMPLEX
Function / homology
Function and homology information


perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / 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 / positive regulation of focal adhesion disassembly ...perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / 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 / positive regulation of focal adhesion disassembly / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / interleukin-18-mediated signaling pathway / myeloid leukocyte migration / autosome genomic imprinting / phosphatidylinositol 3-kinase complex / T follicular helper cell differentiation / PI3K events in ERBB4 signaling / cellular response to hydrostatic pressure / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of cellular respiration / neurotrophin TRKA receptor binding / positive regulation of protein localization to membrane / Activated NTRK2 signals through PI3K / cis-Golgi network / negative regulation of fibroblast apoptotic process / Activated NTRK3 signals through PI3K / ErbB-3 class receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / phosphatidylinositol 3-kinase complex, class IB / vasculature development / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / cardiac muscle cell contraction / RHOD GTPase cycle / RHOF GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / kinase activator activity / Nephrin family interactions / anoikis / Signaling by LTK in cancer / phosphatidylinositol-3-phosphate biosynthetic process / positive regulation of leukocyte migration / Signaling by LTK / MET activates PI3K/AKT signaling / PI3K/AKT activation / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / negative regulation of stress fiber assembly / RND1 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / positive regulation of filopodium assembly / RND2 GTPase cycle / phosphatidylinositol 3-kinase / vascular endothelial growth factor signaling pathway / RND3 GTPase cycle / relaxation of cardiac muscle / insulin binding / growth hormone receptor signaling pathway / 1-phosphatidylinositol-3-kinase activity / Signaling by ALK / RHOV GTPase cycle / PI-3K cascade:FGFR3 / RHOB GTPase cycle / natural killer cell mediated cytotoxicity / negative regulation of macroautophagy / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / GP1b-IX-V activation signalling / PI-3K cascade:FGFR2 / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / negative regulation of osteoclast differentiation / response to dexamethasone / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / CDC42 GTPase cycle / negative regulation of anoikis / RET signaling / PI3K events in ERBB2 signaling / protein kinase activator activity / insulin receptor substrate binding / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / extrinsic apoptotic signaling pathway via death domain receptors / PI3K Cascade / RHOG GTPase cycle / intercalated disc / regulation of multicellular organism growth / negative regulation of cell-matrix adhesion / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / positive regulation of TOR signaling / RAC2 GTPase cycle
Similarity search - Function
Helix Hairpins - #1490 / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 ...Helix Hairpins - #1490 / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Phosphatidylinositol 3-kinase, accessory domain (PIK) / 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. / Rho GTPase activation protein / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / C2 domain / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Helix Hairpins / Alpha Horseshoe / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
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 / molecular replacement / Resolution: 3.05 Å
AuthorsHuang, C. / Gabelli, S.B. / Amzel, L.M.
CitationJournal: Science / Year: 2007
Title: The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations.
Authors: Huang, C.H. / Mandelker, D. / Schmidt-Kittler, O. / Samuels, Y. / Velculescu, V.E. / Kinzler, K.W. / Vogelstein, B. / Gabelli, S.B. / Amzel, L.M.
History
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)161,4902
Polymers161,4902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.058, 117.050, 151.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform / PI3-kinase p110 subunit alpha / PtdIns-3- kinase p110 / PI3K


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 HTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: P42336, phosphatidylinositol-4,5-bisphosphate 3-kinase
#2: Protein Phosphatidylinositol 3-kinase regulatory subunit alpha / PI3-kinase p85 subunit alpha / PtdIns-3-kinase p85-alpha / PI3K


Mass: 33666.961 Da / Num. of mol.: 1 / Fragment: UNP residues 322-600
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Plasmid: pFastBac 1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P27986

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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: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: Sodium Formate, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.081 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.081 Å / Relative weight: 1
ReflectionResolution: 3.05→46.4 Å / Num. obs: 38994 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 80.3 Å2 / Rsym value: 0.072 / Net I/σ(I): 9.4
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3367 / Rsym value: 0.433 / % possible all: 88.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
AMoREphasing
REFMACrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→46.37 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.872 / SU B: 24.793 / SU ML: 0.438 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.508 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.323 2000 5.1 %RANDOM
Rwork0.263 ---
obs0.267 38888 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.662 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--2.39 Å20 Å2
3----3.32 Å2
Refinement stepCycle: LAST / Resolution: 3.05→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9365 0 0 0 9365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229566
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.96312902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.04651127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33824.214477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.696151806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1771566
X-RAY DIFFRACTIONr_chiral_restr0.1080.21399
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027172
X-RAY DIFFRACTIONr_nbd_refined0.2550.25035
X-RAY DIFFRACTIONr_nbtor_refined0.3190.26415
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2330
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.23
X-RAY DIFFRACTIONr_mcbond_it0.7625813
X-RAY DIFFRACTIONr_mcangle_it1.42939194
X-RAY DIFFRACTIONr_scbond_it5.602104232
X-RAY DIFFRACTIONr_scangle_it8.658153708
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 100 -
Rwork0.3 2177 -
all-2277 -
obs--79.26 %
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)
18.05371.608-2.80596.15450.5463.30640.23290.25690.8415-0.4011-0.2859-0.4547-0.11221.84160.053-0.03490.06740.05150.96070.2937-0.2971104.05667.293109.279
23.1905-0.99110.21164.2572-0.87645.43360.07990.2287-0.87950.34060.0881-0.1251.4702-0.375-0.1680.74670.2426-0.03140.6923-0.2845-0.039277.1842.36670.676
315.06530.30491.78315.1531-1.79066.78350.04760.5965-0.1387-0.20570.1411.29770.3178-0.8475-0.18860.07740.04490.02511.127-0.3602-0.271449.63656.47966.702
418.50425.0092-6.05542.43693.418725.64940.00591.6951.19380.07930.44531.5653-0.3949-1.9854-0.4512-0.03890.06280.15950.6168-0.04460.26432.98459.934101.175
511.8958-2.269917.00173.10320.81530.4702-0.6553-0.48250.7865-0.2680.24250.94531.5071-4.16010.41280.1409-0.27710.06450.8644-0.31480.490435.66649.41294.096
612.32435.87472.61874.43721.52192.7320.094-0.5446-1.0543-0.2977-0.1208-0.17050.85640.0760.02680.94480.56350.0850.60450.12750.01684.96839.76799.088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA20 - 10548 - 133
2X-RAY DIFFRACTION2AA330 - 498358 - 526
3X-RAY DIFFRACTION3AA528 - 572556 - 600
4X-RAY DIFFRACTION4AA973 - 9881001 - 1016
5X-RAY DIFFRACTION5AA1031 - 10491059 - 1077
6X-RAY DIFFRACTION6BB442 - 600121 - 279

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