+Open data
-Basic information
Entry | Database: PDB / ID: 6d81 | ||||||||||||
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Title | Structure of the Bovine p85a BH domain | ||||||||||||
Components | Phosphatidylinositol 3-kinase regulatory subunit alpha | ||||||||||||
Keywords | SIGNALING PROTEIN / GAP protein | ||||||||||||
Function / homology | Function and homology information Signaling by ALK / MET activates PI3K/AKT signaling / RHOC GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle / FLT3 Signaling ...Signaling by ALK / MET activates PI3K/AKT signaling / RHOC GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle / FLT3 Signaling / RND3 GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / PI3K events in ERBB4 signaling / Interleukin-7 signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / IRS-mediated signalling / GPVI-mediated activation cascade / Signaling by SCF-KIT / Downstream signal transduction / PI3K/AKT activation / Role of phospholipids in phagocytosis / Tie2 Signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Costimulation by the CD28 family / CD28 dependent PI3K/Akt signaling / RAF/MAP kinase cascade / Interleukin receptor SHC signaling / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / PI3K Cascade / PIP3 activates AKT signaling / GP1b-IX-V activation signalling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Synthesis of PIPs at the plasma membrane / RHOA GTPase cycle / RHOF GTPase cycle / DAP12 signaling / RHOU GTPase cycle / RHOV GTPase cycle / Regulation of signaling by CBL / Downstream TCR signaling / RHOG GTPase cycle / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / phosphatidylinositol 3-kinase regulator activity / phosphatidylinositol 3-kinase activator activity / 1-phosphatidylinositol-3-kinase regulator activity / ErbB-3 class receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / positive regulation of endoplasmic reticulum unfolded protein response / phosphatidylinositol 3-kinase complex, class IA / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex / Extra-nuclear estrogen signaling / G alpha (q) signalling events / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / insulin receptor substrate binding / phosphatidylinositol 3-kinase binding / insulin-like growth factor receptor binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to endoplasmic reticulum stress / substrate adhesion-dependent cell spreading / insulin-like growth factor receptor signaling pathway / positive regulation of RNA splicing / positive regulation of glucose import / positive regulation of protein localization to plasma membrane / insulin receptor binding / positive regulation of protein import into nucleus / cellular response to insulin stimulus / protein transport / insulin receptor signaling pathway / protein stabilization / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 Å | ||||||||||||
Authors | Moore, S.A. / Marshall, J.D. / Anderson, D.H. | ||||||||||||
Funding support | Canada, 3items
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Citation | Journal: Sci Rep / Year: 2018 Title: Patient-derived mutations within the N-terminal domains of p85 alpha impact PTEN or Rab5 binding and regulation. Authors: Mellor, P. / Marshall, J.D.S. / Ruan, X. / Whitecross, D.E. / Ross, R.L. / Knowles, M.A. / Moore, S.A. / Anderson, D.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d81.cif.gz | 148.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d81.ent.gz | 118.3 KB | Display | PDB format |
PDBx/mmJSON format | 6d81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/6d81 ftp://data.pdbj.org/pub/pdb/validation_reports/d8/6d81 | HTTPS FTP |
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-Related structure data
Related structure data | 6d82C 6d85C 6d86C 6d87C 1pbwS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 21909.146 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: PIK3R1 / Plasmid: PGEX-6P3 Details (production host): Glutathione S Transferase fusion protein Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23727 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 4.21 Å3/Da / Density % sol: 70.8 % / Description: Prisms |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.5 M Li2SO4, pH 6.0, 100mM Na Cacodylate |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.987 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 25, 2015 / Details: Toroidal Focusing Mirror |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.248→46.9 Å / Num. obs: 35631 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 2.248→2.309 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 3 / Num. unique obs: 2519 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PBW Resolution: 2.248→46.889 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.22 / Details: Maximum Likelihood refinement using PHENIX
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.248→46.889 Å
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Refine LS restraints |
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LS refinement shell |
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