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Yorodumi- PDB-7rnu: nSH2 domain of p85-beta subunit of phosphatidylinositol 3-kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rnu | ||||||
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Title | nSH2 domain of p85-beta subunit of phosphatidylinositol 3-kinase in complex with an actin peptide with phosphorylated tyrosine 53 | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / phosphorylated tyrosine binding protein / actin peptide | ||||||
Function / homology | Function and homology information : / skeletal muscle fiber adaptation / IRS-mediated signalling / : / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / RHOF GTPase cycle / regulation of stress fiber assembly / RHOD GTPase cycle ...: / skeletal muscle fiber adaptation / IRS-mediated signalling / : / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / RHOF GTPase cycle / regulation of stress fiber assembly / RHOD GTPase cycle / Striated Muscle Contraction / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / Nephrin family interactions / Signaling by LTK in cancer / response to steroid hormone / RND1 GTPase cycle / Costimulation by the CD28 family / Signaling by LTK / RND2 GTPase cycle / PI3K/AKT activation / RND3 GTPase cycle / negative regulation of MAPK cascade / Signaling by ALK / RHOB GTPase cycle / myosin binding / mesenchyme migration / RHOJ GTPase cycle / 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 / RET signaling / positive regulation of cell adhesion / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of protein localization to plasma membrane / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / skeletal muscle fiber development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / muscle contraction / stress fiber / response to mechanical stimulus / Tie2 Signaling / GPVI-mediated activation cascade / RAC1 GTPase cycle / phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphotyrosine residue binding / Interleukin-7 signaling / sarcomere / Downstream signal transduction / response to endoplasmic reticulum stress / B cell differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / filopodium / regulation of autophagy / actin filament / Regulation of signaling by CBL / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by SCF-KIT / cellular response to insulin stimulus / structural constituent of cytoskeleton / receptor tyrosine kinase binding / ADP binding / Constitutive Signaling by Aberrant PI3K in Cancer / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / PIP3 activates AKT signaling / Signaling by ALK fusions and activated point mutants / actin cytoskeleton / protein transport / Downstream TCR signaling / insulin receptor signaling pathway / DAP12 signaling / lamellipodium / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein phosphatase binding / cell body / G alpha (q) signalling events / Extra-nuclear estrogen signaling / blood microparticle / hydrolase activity / immune response / protein heterodimerization activity / focal adhesion / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Dai, S. / Horton, J.R. / Cheng, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rnu.cif.gz | 142.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rnu.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 7rnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rnu_validation.pdf.gz | 494.1 KB | Display | wwPDB validaton report |
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Full document | 7rnu_full_validation.pdf.gz | 497.5 KB | Display | |
Data in XML | 7rnu_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 7rnu_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/7rnu ftp://data.pdbj.org/pub/pdb/validation_reports/rn/7rnu | HTTPS FTP |
-Related structure data
Related structure data | 7rnsC 7rnvC 2iuiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 | 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 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.27 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25% w/v PEG1500, 100 mM MIB, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.45→1.5 Å / Num. unique obs: 4489 / CC1/2: 0.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→34.92 Å
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Refine LS restraints |
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LS refinement shell |
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