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- PDB-6d81: Structure of the Bovine p85a BH domain -

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Basic information

Entry
Database: PDB / ID: 6d81
TitleStructure of the Bovine p85a BH domain
ComponentsPhosphatidylinositol 3-kinase regulatory subunit alpha
KeywordsSIGNALING PROTEIN / GAP protein
Function / homology
Function and homology information


Signaling by ALK / MET activates PI3K/AKT signaling / RHOC GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle / RHOF GTPase cycle ...Signaling by ALK / MET activates PI3K/AKT signaling / RHOC GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle / RHOF GTPase cycle / FLT3 Signaling / RND3 GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / PI3K events in ERBB4 signaling / Interleukin-7 signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / IRS-mediated signalling / GPVI-mediated activation cascade / Signaling by SCF-KIT / Downstream signal transduction / PI3K/AKT activation / Role of phospholipids in phagocytosis / Tie2 Signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Costimulation by the CD28 family / CD28 dependent PI3K/Akt signaling / RAF/MAP kinase cascade / Interleukin receptor SHC signaling / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / PI3K Cascade / PIP3 activates AKT signaling / GP1b-IX-V activation signalling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Synthesis of PIPs at the plasma membrane / RHOA GTPase cycle / DAP12 signaling / RHOU GTPase cycle / RHOV GTPase cycle / RHOG GTPase cycle / Regulation of signaling by CBL / Downstream TCR signaling / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / phosphatidylinositol 3-kinase regulator activity / phosphatidylinositol 3-kinase activator activity / 1-phosphatidylinositol-3-kinase regulator activity / ErbB-3 class receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / positive regulation of endoplasmic reticulum unfolded protein response / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex / Extra-nuclear estrogen signaling / G alpha (q) signalling events / phosphatidylinositol 3-kinase complex, class IA / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / insulin receptor substrate binding / phosphatidylinositol 3-kinase binding / insulin-like growth factor receptor binding / response to endoplasmic reticulum stress / substrate adhesion-dependent cell spreading / positive regulation of RNA splicing / insulin-like growth factor receptor signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein localization to plasma membrane / positive regulation of glucose import / insulin receptor binding / positive regulation of protein import into nucleus / cellular response to insulin stimulus / protein transport / insulin receptor signaling pathway / protein stabilization / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / 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 / Rho GTPase-activating protein domain / RhoGAP domain ...Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / 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 / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 Å
AuthorsMoore, S.A. / Marshall, J.D. / Anderson, D.H.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP84277 Canada
Canadian Institutes of Health Research (CIHR)MOP126155 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN262138 Canada
CitationJournal: Sci Rep / Year: 2018
Title: Patient-derived mutations within the N-terminal domains of p85 alpha impact PTEN or Rab5 binding and regulation.
Authors: Mellor, P. / Marshall, J.D.S. / Ruan, X. / Whitecross, D.E. / Ross, R.L. / Knowles, M.A. / Moore, S.A. / Anderson, D.H.
History
DepositionApr 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Phosphatidylinositol 3-kinase regulatory subunit alpha
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1065
Polymers43,8182
Non-polymers2883
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-33 kcal/mol
Surface area17470 Å2
2
A: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0052
Polymers21,9091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1013
Polymers21,9091
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.825, 91.737, 93.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 21909.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PIK3R1 / Plasmid: PGEX-6P3
Details (production host): Glutathione S Transferase fusion protein
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23727
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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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: 4.21 Å3/Da / Density % sol: 70.8 % / Description: Prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.5 M Li2SO4, pH 6.0, 100mM Na Cacodylate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.987 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 25, 2015 / Details: Toroidal Focusing Mirror
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.248→46.9 Å / Num. obs: 35631 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 24.2
Reflection shellResolution: 2.248→2.309 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 3 / Num. unique obs: 2519 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBW

1pbw


Resolution: 2.248→46.889 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.22 / Details: Maximum Likelihood refinement using PHENIX
RfactorNum. reflection% reflection
Rfree0.2128 1892 5.32 %
Rwork0.1916 --
obs0.1927 35588 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.248→46.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 15 101 2971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032932
X-RAY DIFFRACTIONf_angle_d0.7053994
X-RAY DIFFRACTIONf_dihedral_angle_d12.831818
X-RAY DIFFRACTIONf_chiral_restr0.04482
X-RAY DIFFRACTIONf_plane_restr0.005498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2485-2.30470.23751280.21632323X-RAY DIFFRACTION97
2.3047-2.3670.26281480.2222345X-RAY DIFFRACTION99
2.367-2.43670.23491500.21812345X-RAY DIFFRACTION99
2.4367-2.51530.23531470.21972380X-RAY DIFFRACTION99
2.5153-2.60520.22031400.2072379X-RAY DIFFRACTION99
2.6052-2.70950.24241520.20892334X-RAY DIFFRACTION99
2.7095-2.83280.24121020.2072419X-RAY DIFFRACTION100
2.8328-2.98210.22081090.21022424X-RAY DIFFRACTION99
2.9821-3.16890.25381150.20922423X-RAY DIFFRACTION99
3.1689-3.41350.22631060.20822442X-RAY DIFFRACTION100
3.4135-3.75690.21591460.1932428X-RAY DIFFRACTION100
3.7569-4.30020.18031840.16242388X-RAY DIFFRACTION100
4.3002-5.41660.16591420.15142476X-RAY DIFFRACTION100
5.4166-46.89920.22711230.19432590X-RAY DIFFRACTION99

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