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- PDB-1qad: Crystal Structure of the C-Terminal SH2 Domain of the P85 alpha R... -

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Basic information

Entry
Database: PDB / ID: 1qad
TitleCrystal Structure of the C-Terminal SH2 Domain of the P85 alpha Regulatory Subunit of Phosphoinositide 3-Kinase: An SH2 domain mimicking its own substrate
ComponentsPI3-KINASE P85 ALPHA SUBUNIT
KeywordsTRANSFERASE / PHOPHOTYROSINE-BINDING DOMAIN / SUBSTRATE MIMICKING
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 / Regulation of signaling by CBL / Downstream TCR signaling / RHOG GTPase cycle / 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, class IA / phosphatidylinositol 3-kinase complex / Extra-nuclear estrogen signaling / G alpha (q) signalling events / 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 glucose import / positive regulation of protein localization to plasma membrane / 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 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 ...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 / SHC Adaptor 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsHoedemaeker, P.J. / Siegal, G. / Roe, M. / Driscoll, P.C. / Abrahams, J.P.A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the C-terminal SH2 domain of the p85alpha regulatory subunit of phosphoinositide 3-kinase: an SH2 domain mimicking its own substrate.
Authors: Hoedemaeker, F.J. / Siegal, G. / Roe, S.M. / Driscoll, P.C. / Abrahams, J.P.
History
DepositionFeb 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PI3-KINASE P85 ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)12,6151
Polymers12,6151
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.680, 46.920, 62.980
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 PI3-KINASE P85 ALPHA SUBUNIT


Mass: 12615.052 Da / Num. of mol.: 1 / Fragment: C-TERMINAL SH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P23727
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.427 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 277 K / Method: spontaneous crystallisation / pH: 7.5
Details: TRIS-HCL, NACL, EDTA, DTT, pH 7.5, SPONTANEOUS CRYSTALLISATION, temperature 277.0K
Components of the solutions
IDNameCrystal-IDSol-ID
11mM protein (~13mg/ml)11
250mM TRIS-HCL12
350mM NaCl12
41mM DTT12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Eck, M.J., (1993) Nature, 362, 87. / pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125-35 %PEG20001reservoircan be replaced by PEG4000 or PEG8000
250 mM1reservoirMgCl2
3100 mMsodium acetate1reservoirpH4.6
450 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.8→23.44 Å / Num. all: 10947 / Num. obs: 10947 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 18 Å2 / Net I/σ(I): 7.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3 % / Mean I/σ(I) obs: 10.2 / % possible all: 84.5
Reflection
*PLUS
Num. measured all: 37237 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 84.5 % / Num. unique obs: 677 / Num. measured obs: 2058 / Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
WARPmodel building
REFMACrefinement
CCP4(SCALA)data scaling
ARP/wARPmodel building
RefinementStarting model: 1BFJ

1bfj


Resolution: 1.8→23.44 Å / SU B: 2.3668 / SU ML: 0.07628 / Cross valid method: Rfree / ESU R Free: 0.14209 / Stereochemistry target values: ENGH & HUBER
Details: CONJUGATED DIRECTION METHOD WITH MAXIMUM LIKELYHOOD TARGET (REFMAC_aniso)
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1121 -RANDOM
Rwork0.158 ---
all-10947 --
obs-9826 88.6 %-
Refinement stepCycle: LAST / Resolution: 1.8→23.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 0 185 1015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / Rfactor Rfree: 0.231 / Num. reflection Rfree: 135 / Num. reflection Rwork: 1159 / Rfactor obs: 0.118

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