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- PDB-7rns: nSH2 domain of p85-alpha subunit of phosphatidylinositol 3-kinase... -

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Basic information

Entry
Database: PDB / ID: 7rns
TitlenSH2 domain of p85-alpha subunit of phosphatidylinositol 3-kinase in complex with an actin peptide with phosphorylated tyrosine 53
Components
  • Actin, alpha skeletal muscle
  • Isoform 2 of Phosphatidylinositol 3-kinase regulatory subunit alpha
KeywordsPEPTIDE BINDING PROTEIN / phosphorylated tyrosine binding protein / actin peptide
Function / homology
Function and homology information


skeletal muscle fiber adaptation / perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / : / interleukin-18-mediated signaling pathway ...skeletal muscle fiber adaptation / perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / 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 / : / Activated NTRK3 signals through PI3K / cis-Golgi network / ErbB-3 class receptor binding / RHOF GTPase cycle / kinase activator activity / transmembrane receptor protein tyrosine kinase adaptor activity / RHOD GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / positive regulation of endoplasmic reticulum unfolded protein response / Striated Muscle Contraction / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / Nephrin family interactions / response to steroid hormone / RND1 GTPase cycle / Costimulation by the CD28 family / positive regulation of leukocyte migration / MET activates PI3K/AKT signaling / RND2 GTPase cycle / PI3K/AKT activation / positive regulation of filopodium assembly / RND3 GTPase cycle / negative regulation of stress fiber assembly / growth hormone receptor signaling pathway / insulin binding / RHOV GTPase cycle / negative regulation of cell-matrix adhesion / Signaling by ALK / RHOB GTPase cycle / GP1b-IX-V activation signalling / myosin binding / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / mesenchyme migration / PI-3K cascade:FGFR2 / RHOJ GTPase cycle / PI-3K cascade:FGFR4 / 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 / skeletal muscle thin filament assembly / phosphatidylinositol phosphate biosynthetic process / striated muscle thin filament / CDC42 GTPase cycle / RHOU GTPase cycle / PI3K events in ERBB2 signaling / T cell differentiation / RET signaling / 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 / RAC2 GTPase cycle / RAC3 GTPase cycle / Role of phospholipids in phagocytosis / GAB1 signalosome / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / phosphatidylinositol 3-kinase binding / skeletal muscle fiber development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / positive regulation of lamellipodium assembly / Signaling by FGFR4 in disease / response to mechanical stimulus / stress fiber / Signaling by FLT3 ITD and TKD mutants / Signaling by FGFR3 in disease / Tie2 Signaling / GPVI-mediated activation cascade / Signaling by FGFR2 in disease / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / Interleukin-7 signaling / phosphotyrosine residue binding
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 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / SH2 domain / Src homology 2 (SH2) domain profile. / ATPase, nucleotide binding domain / 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
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit alpha / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsDai, S. / Horton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: To Be Published
Title: The Functional Analysis of a Major Tyrosine Phosphorylation Site on Actin
Authors: Amelie, A. / Dai, S. / Shen, X. / Horton, J.R. / Zhang, X. / Cheng, X.
History
DepositionJul 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Phosphatidylinositol 3-kinase regulatory subunit alpha
B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9528
Polymers14,5802
Non-polymers3726
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-3 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.795, 46.536, 50.089
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 Isoform 2 of 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: 13516.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27986
#2: Protein/peptide Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 1063.975 Da / Num. of mol.: 1 / Fragment: UNP residues 52-60 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68133
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.75 Å3/Da / Density % sol: 29.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M cadmium sulfate hydrate, 0.1 M HEPES, pH 7.5, 1.0 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.14→26.9 Å / Num. obs: 37579 / % possible obs: 97.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 7.76 Å2 / CC1/2: 0.981 / Net I/σ(I): 13.8
Reflection shellResolution: 1.14→1.18 Å / Num. unique obs: 3027 / CC1/2: 0.512

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CrysalisProdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IUI

2iui


Resolution: 1.14→26.9 Å / SU ML: 0.103 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.5045
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.147 1868 4.97 %
Rwork0.1334 35680 -
obs0.1341 37548 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.69 Å2
Refinement stepCycle: LAST / Resolution: 1.14→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 24 196 1193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921093
X-RAY DIFFRACTIONf_angle_d1.21381477
X-RAY DIFFRACTIONf_chiral_restr0.0831152
X-RAY DIFFRACTIONf_plane_restr0.0074194
X-RAY DIFFRACTIONf_dihedral_angle_d26.3692414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.170.3277930.42062051X-RAY DIFFRACTION73.35
1.17-1.20.31721500.25852684X-RAY DIFFRACTION97.35
1.2-1.240.15331460.14632716X-RAY DIFFRACTION98.32
1.24-1.280.16441370.12432773X-RAY DIFFRACTION99.08
1.28-1.330.17021540.12092764X-RAY DIFFRACTION99.45
1.33-1.40.14661380.11732784X-RAY DIFFRACTION99.66
1.4-1.470.15761500.10922788X-RAY DIFFRACTION99.73
1.47-1.560.12511430.10462808X-RAY DIFFRACTION99.93
1.56-1.680.12061460.1112816X-RAY DIFFRACTION100
1.68-1.850.13521510.11252815X-RAY DIFFRACTION100
1.85-2.120.12011510.11272827X-RAY DIFFRACTION100
2.12-2.670.14411490.1262862X-RAY DIFFRACTION100
2.67-26.90.13581600.13892992X-RAY DIFFRACTION99.68

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