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- PDB-3mtt: Crystal structure of iSH2 domain of human p85beta, Northeast Stru... -

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Basic information

Entry
Database: PDB / ID: 3mtt
TitleCrystal structure of iSH2 domain of human p85beta, Northeast Structural Genomics Consortium Target HR5531C
ComponentsPhosphatidylinositol 3-kinase regulatory subunit beta
KeywordsSIGNALING PROTEIN / PROTEIN BINDING / PI3-kinase subunit p85-beta / inter-SH2 domain / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


IRS-mediated signalling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of stress fiber assembly / Co-stimulation by ICOS / RHOD GTPase cycle / RHOF GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions ...IRS-mediated signalling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of stress fiber assembly / Co-stimulation by ICOS / RHOD GTPase cycle / RHOF GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions / Signaling by LTK in cancer / Signaling by LTK / PI3K/AKT activation / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / Signaling by ALK / RHOB GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / CDC42 GTPase cycle / RET signaling / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / RAC2 GTPase cycle / Role of LAT2/NTAL/LAB on calcium mobilization / RAC3 GTPase cycle / Interleukin receptor SHC signaling / Role of phospholipids in phagocytosis / negative regulation of MAPK cascade / regulation of protein localization to plasma membrane / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / GPVI-mediated activation cascade / Tie2 Signaling / RAC1 GTPase cycle / phosphotyrosine residue binding / Interleukin-7 signaling / positive regulation of cell adhesion / Downstream signal transduction / B cell differentiation / response to endoplasmic reticulum stress / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of signaling by CBL / Signaling by SCF-KIT / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / cellular response to insulin stimulus / Constitutive Signaling by Aberrant PI3K in Cancer / Signaling by ALK fusions and activated point mutants / insulin receptor signaling pathway / DAP12 signaling / protein transport / Downstream TCR signaling / PIP3 activates AKT signaling / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein phosphatase binding / G alpha (q) signalling events / Extra-nuclear estrogen signaling / regulation of autophagy / immune response / protein heterodimerization activity / focal adhesion / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 domain / Helix Hairpins - #1490 / 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 beta, SH3 domain / Helix Hairpins - #1490 / 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 / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGuan, R. / Schauder, C. / Ma, L.C. / Krug, R.M. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of the iSH2 domain of human phosphatidylinositol 3-kinase p85beta subunit reveals conformational plasticity in the interhelical turn region
Authors: Schauder, C. / Ma, L.C. / Krug, R.M. / Montelione, G.T. / Guan, R.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 3-kinase regulatory subunit beta


Theoretical massNumber of molelcules
Total (without water)22,7491
Polymers22,7491
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.588, 174.588, 102.699
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-6-

HOH

21A-9-

HOH

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Components

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


Mass: 22748.605 Da / Num. of mol.: 1 / Fragment: iSH2 domain, residues 433-610
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R2 / Plasmid: pet21C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O00459
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 6.62 Å3/Da / Density % sol: 81.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.5 M Sodium Malonate, 0.1 M HEPES, , pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2010
RadiationMonochromator: Si(iii) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.3→48.6 Å / Num. all: 9170 / Num. obs: 9161 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 22.1 % / Biso Wilson estimate: 110 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 39
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 22.5 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 6.83 / Num. unique all: 897 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_377)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L4Q chain D

3l4q


Resolution: 3.3→48.6 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 427 4.77 %random
Rwork0.2487 ---
obs0.2501 8955 97.51 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.281 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.4193 Å2-0 Å20 Å2
2---6.4193 Å20 Å2
3---12.8386 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 0 14 1399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031402
X-RAY DIFFRACTIONf_angle_d0.6251868
X-RAY DIFFRACTIONf_dihedral_angle_d15.461573
X-RAY DIFFRACTIONf_chiral_restr0.05194
X-RAY DIFFRACTIONf_plane_restr0.002246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.297-3.77390.35241430.32312718X-RAY DIFFRACTION95
3.7739-4.7540.26571490.25242837X-RAY DIFFRACTION98
4.754-48.62720.2591350.2242973X-RAY DIFFRACTION99

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