[English] 日本語
Yorodumi
- PDB-7rnu: nSH2 domain of p85-beta subunit of phosphatidylinositol 3-kinase ... -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of actin filament polymerization / IRS-mediated signalling / 1-phosphatidylinositol-3-kinase regulator activity / Formation of the dystrophin-glycoprotein complex (DGC) / phosphatidylinositol 3-kinase regulatory subunit binding / cellular response to potassium ion / regulation of stress fiber assembly / Co-stimulation by ICOS / RHOD GTPase cycle ...skeletal muscle fiber adaptation / regulation of actin filament polymerization / IRS-mediated signalling / 1-phosphatidylinositol-3-kinase regulator activity / Formation of the dystrophin-glycoprotein complex (DGC) / phosphatidylinositol 3-kinase regulatory subunit binding / cellular response to potassium ion / regulation of stress fiber assembly / Co-stimulation by ICOS / RHOD GTPase cycle / Striated Muscle Contraction / 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 / response to steroid hormone / RND2 GTPase cycle / RND3 GTPase cycle / Signaling by ALK / RHOB GTPase cycle / myosin binding / RHOJ GTPase cycle / intracellular glucose homeostasis / mesenchyme migration / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / CDC42 GTPase cycle / RET signaling / striated muscle thin filament / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / skeletal muscle thin filament assembly / PI3K Cascade / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / Role of LAT2/NTAL/LAB on calcium mobilization / RAC2 GTPase cycle / 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 / response to mechanical stimulus / stress fiber / skeletal muscle fiber development / GPVI-mediated activation cascade / Tie2 Signaling / muscle contraction / 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 / sarcomere / filopodium / actin filament / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of signaling by CBL / Signaling by SCF-KIT / ADP binding / receptor tyrosine kinase binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / 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 / lamellipodium / actin cytoskeleton / cell body / 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 / blood microparticle / Extra-nuclear estrogen signaling / hydrolase activity / regulation of autophagy / immune response / protein heterodimerization activity / focal adhesion / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome
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. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / ATPase, nucleotide binding domain / 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more