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Yorodumi- PDB-2v1y: Structure of a phosphoinositide 3-kinase alpha adaptor-binding do... -
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-Basic information
Entry | Database: PDB / ID: 2v1y | ||||||
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Title | Structure of a phosphoinositide 3-kinase alpha adaptor-binding domain (ABD) in a complex with the iSH2 domain from p85 alpha | ||||||
Components |
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Keywords | TRANSFERASE / KINASE / CANCER / SH2 DOMAIN / SH3 DOMAIN / ONCOGENIC MUTATIONS / HOST-VIRUS INTERACTION / PHOSPHORYLATION / DISEASE MUTATION / PHOSPHOINOSITIDE / PHOSPHOLIPID / PHOSPHOLIPID SIGNALLING / PHOSPHOINOSITIDE 3-KINASE / SIGNAL TRANSDUCTION | ||||||
Function / homology | Function and homology information : / : / : / : / PI3K events in ERBB4 signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / IRS-mediated signalling / GPVI-mediated activation cascade ...: / : / : / : / PI3K events in ERBB4 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 / Interleukin receptor SHC signaling / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / PI3K Cascade / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Synthesis of PIPs at the plasma membrane / DAP12 signaling / Regulation of signaling by CBL / perinuclear endoplasmic reticulum membrane / RET signaling / regulation of toll-like receptor 4 signaling pathway / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / IRS-mediated signalling / positive regulation of gene expression via chromosomal CpG island demethylation / positive regulation of focal adhesion disassembly / 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 / negative regulation of fibroblast apoptotic process / kinase activator activity / phosphatidylinositol 3-kinase complex, class IB / transmembrane receptor protein tyrosine kinase adaptor activity / RHOF GTPase cycle / RHOD GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / regulation of cellular respiration / positive regulation of endoplasmic reticulum unfolded protein response / phosphatidylinositol 3-kinase complex, class IA / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex / Nephrin family interactions / Signaling by LTK in cancer / PI3K events in ERBB2 signaling / RND1 GTPase cycle / Costimulation by the CD28 family / Signaling by LTK / positive regulation of leukocyte migration / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / Extra-nuclear estrogen signaling / MET activates PI3K/AKT signaling / RND2 GTPase cycle / PI3K/AKT activation / positive regulation of filopodium assembly / RND3 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / negative regulation of stress fiber assembly / growth hormone receptor signaling pathway / G alpha (q) signalling events / natural killer cell mediated cytotoxicity / insulin binding / phosphatidylinositol-3-phosphate biosynthetic process / RHOV GTPase cycle / 1-phosphatidylinositol-3-kinase activity / Signaling by ALK / negative regulation of cell-matrix adhesion / RHOB GTPase cycle / GP1b-IX-V activation signalling / GAB1 signalosome / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR2 / protein kinase activator activity / PI-3K cascade:FGFR4 / RHOC GTPase cycle / RHOJ GTPase cycle / PI-3K cascade:FGFR1 / negative regulation of osteoclast differentiation Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Miled, N. / Yan, Y. / Hon, W.C. / Perisic, O. / Zvelebil, M. / Inbar, Y. / Schneidman-Duhovny, D. / Wolfson, H.J. / Backer, J.M. / Williams, R.L. | ||||||
Citation | Journal: Science / Year: 2007 Title: Mechanism of Two Classes of Cancer Mutations in the Phosphoinositide 3-Kinase Catalytic Subunit. Authors: Miled, N. / Yan, Y. / Hon, W.C. / Perisic, O. / Zvelebil, M. / Inbar, Y. / Schneidman-Duhovny, D. / Wolfson, H.J. / Backer, J.M. / Williams, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v1y.cif.gz | 65 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v1y.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 2v1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v1y_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 2v1y_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 2v1y_validation.xml.gz | 11 KB | Display | |
Data in CIF | 2v1y_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/2v1y ftp://data.pdbj.org/pub/pdb/validation_reports/v1/2v1y | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12821.479 Da / Num. of mol.: 1 / Fragment: ADAPTOR-BINDING DOMAIN, RESIDUES 1-108 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) Description: CHAIN A IS THE ADAPTOR-BINDING DOMAIN FROM BOVINE P110 ALPHA Plasmid: POPCG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) References: UniProt: P32871, phosphatidylinositol-4,5-bisphosphate 3-kinase |
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#2: Protein | Mass: 21223.402 Da / Num. of mol.: 1 / Fragment: INTER-SH2 DOMAIN (ISH2), RESIDUES 431-600 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: CHAIN B IS THE ISH2 DOMAIN FROM HUMAN P85 ALPHA Plasmid: POPCG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) References: UniProt: P27986, phosphatidylinositol-4,5-bisphosphate 3-kinase |
#3: Water | ChemComp-HOH / |
Compound details | PHOSPHORYLATES PTDINS, PTDINS4P AND PTDINS(4,5)P2. BINDS TO ACTIVATED (PHOSPHORYLATED) PROTEIN-TYR ...PHOSPHORYL |
Sequence details | ADAPTOR-BINDING DOMAIN, RESIDUES 1-108 RESIDUES 431-600 OF HUMAN P85 ALPHA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43 % |
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Crystal grow | pH: 7 Details: 0.2M MG(NO3)2, 20% PEG3350 (HAMPTON), 5MM TRIS-HCL PH 7.0 (25C), 5% GLYCEROL AND 5MM FRESH DTT |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794,0.9393 | |||||||||
Detector | Type: ADSC CCD / Detector: CCD / Details: BENT MIRROR | |||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→47.67 Å / Num. obs: 10926 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.53 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.48 | |||||||||
Reflection shell | Resolution: 2.4→2.42 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.32 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2.4→47.67 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.882 / SU B: 9.151 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.71 / ESU R Free: 0.333 Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→47.67 Å
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