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- PDB-7rnu: nSH2 domain of p85-beta subunit of phosphatidylinositol 3-kinase ... -

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Basic information

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


skeletal muscle fiber adaptation / IRS-mediated signalling / cellular response to organonitrogen compound / regulation of actin filament polymerization / phosphatidylinositol 3-kinase regulatory subunit binding / 1-phosphatidylinositol-3-kinase regulator activity / : / RHOF GTPase cycle / regulation of stress fiber assembly / RHOD GTPase cycle ...skeletal muscle fiber adaptation / IRS-mediated signalling / cellular response to organonitrogen compound / regulation of actin filament polymerization / phosphatidylinositol 3-kinase regulatory subunit binding / 1-phosphatidylinositol-3-kinase regulator activity / : / RHOF GTPase cycle / regulation of stress fiber assembly / RHOD GTPase cycle / Striated Muscle Contraction / phosphatidylinositol 3-kinase complex / Nephrin family interactions / response to steroid hormone / RND1 GTPase cycle / Costimulation by the CD28 family / RND2 GTPase cycle / PI3K/AKT activation / RND3 GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / RHOB GTPase cycle / Signaling by ALK / myosin binding / negative regulation of MAPK cascade / mesenchyme migration / RHOJ GTPase cycle / intracellular glucose homeostasis / skeletal muscle thin filament assembly / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / striated muscle thin filament / phosphatidylinositol phosphate biosynthetic process / CDC42 GTPase cycle / RHOU GTPase cycle / RET signaling / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / positive regulation of cell adhesion / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / skeletal muscle fiber development / regulation of protein localization to plasma membrane / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / response to mechanical stimulus / stress fiber / GPVI-mediated activation cascade / Tie2 Signaling / RAC1 GTPase cycle / Interleukin-7 signaling / phosphotyrosine residue binding / response to endoplasmic reticulum stress / Downstream signal transduction / sarcomere / B cell differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / phosphatidylinositol 3-kinase/protein kinase B signal transduction / muscle contraction / filopodium / regulation of autophagy / actin filament / ADP binding / Regulation of signaling by CBL / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by SCF-KIT / structural constituent of cytoskeleton / 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 / actin cytoskeleton / protein transport / Downstream TCR signaling / PIP3 activates AKT signaling / DAP12 signaling / insulin receptor signaling pathway / lamellipodium / cell body / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / G alpha (q) signalling events / protein phosphatase binding / blood microparticle / Extra-nuclear estrogen signaling / hydrolase activity / immune response / protein heterodimerization activity / focal adhesion / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / ATP binding / nucleus
Similarity search - Function
Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 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 ...Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 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 beta / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 3-kinase regulatory subunit beta
B: Actin, alpha skeletal muscle
C: Phosphatidylinositol 3-kinase regulatory subunit beta
D: Actin, alpha skeletal muscle
E: Phosphatidylinositol 3-kinase regulatory subunit beta
F: Actin, alpha skeletal muscle
G: Phosphatidylinositol 3-kinase regulatory subunit beta
H: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,87016
Polymers56,3748
Non-polymers4978
Water7,278404
1
A: Phosphatidylinositol 3-kinase regulatory subunit beta
B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2805
Polymers14,0932
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-2 kcal/mol
Surface area6360 Å2
MethodPISA
2
C: Phosphatidylinositol 3-kinase regulatory subunit beta
D: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2805
Polymers14,0932
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-2 kcal/mol
Surface area6850 Å2
MethodPISA
3
E: Phosphatidylinositol 3-kinase regulatory subunit beta
F: Actin, alpha skeletal muscle


Theoretical massNumber of molelcules
Total (without water)14,0932
Polymers14,0932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-2 kcal/mol
Surface area6270 Å2
MethodPISA
4
G: Phosphatidylinositol 3-kinase regulatory subunit beta
H: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2184
Polymers14,0932
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-7 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.083, 41.432, 65.875
Angle α, β, γ (deg.)90.000, 100.294, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-426-

TYR

21C-703-

HOH

31C-707-

HOH

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Components

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


Mass: 13029.506 Da / Num. of mol.: 4 / Fragment: nSH2 domain (UNP residues 318-428)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00459
#2: Protein/peptide
Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 1063.975 Da / Num. of mol.: 4 / 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25% w/v PEG1500, 100 mM MIB, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→34.92 Å / Num. obs: 79846 / % possible obs: 89.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 15.07 Å2 / CC1/2: 0.991 / Net I/σ(I): 11.8
Reflection shellResolution: 1.45→1.5 Å / Num. unique obs: 4489 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IUI

2iui


Resolution: 1.45→34.92 Å / SU ML: 0.1734 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4433
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2222 2000 2.51 %
Rwork0.1906 77820 -
obs0.1914 79820 89.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.19 Å2
Refinement stepCycle: LAST / Resolution: 1.45→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3710 0 32 404 4146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523886
X-RAY DIFFRACTIONf_angle_d0.83175275
X-RAY DIFFRACTIONf_chiral_restr0.0724555
X-RAY DIFFRACTIONf_plane_restr0.0047679
X-RAY DIFFRACTIONf_dihedral_angle_d26.28041413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.3259720.30582789X-RAY DIFFRACTION45.08
1.49-1.530.30731020.27253976X-RAY DIFFRACTION64.46
1.53-1.570.29271210.26714722X-RAY DIFFRACTION76.91
1.57-1.620.29711390.25495394X-RAY DIFFRACTION87.41
1.62-1.680.32031500.24885835X-RAY DIFFRACTION94.82
1.68-1.750.25671550.22966032X-RAY DIFFRACTION97.45
1.75-1.830.25461510.22815897X-RAY DIFFRACTION95.36
1.83-1.920.23991580.20386100X-RAY DIFFRACTION98.47
1.92-2.040.2291580.19756178X-RAY DIFFRACTION99.75
2.04-2.20.22761590.19016177X-RAY DIFFRACTION99.5
2.2-2.420.21551590.18676183X-RAY DIFFRACTION99.25
2.42-2.770.22251550.18966038X-RAY DIFFRACTION96.72
2.77-3.490.21621600.17426236X-RAY DIFFRACTION99.39
3.49-34.920.17391610.15516263X-RAY DIFFRACTION97.36

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