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Yorodumi- PDB-1h10: HIGH RESOLUTION STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN OF PR... -
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-Basic information
Entry | Database: PDB / ID: 1h10 | ||||||
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Title | HIGH RESOLUTION STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN OF PROTEIN KINASE B/AKT BOUND TO INS(1,3,4,5)-TETRAKISPHOPHATE | ||||||
Components | RAC-ALPHA SERINE/THREONINE KINASE | ||||||
Keywords | TRANSFERASE / SIGNALLING PROTEIN / PHOSPHOINOSITIDES / PROTEIN KINASE B / PLECKSTRIN / INOSITOL TETRAKISPHOPHATE / PHOSPHORYLATION / SERINE/THREONINE PROTEIN KINASE | ||||||
Function / homology | Function and homology information glycogen cell differentiation involved in embryonic placenta development / regulation of tRNA methylation / response to insulin-like growth factor stimulus / potassium channel activator activity / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / maintenance of protein location in mitochondrion / negative regulation of lymphocyte migration / cellular response to decreased oxygen levels / regulation of type B pancreatic cell development ...glycogen cell differentiation involved in embryonic placenta development / regulation of tRNA methylation / response to insulin-like growth factor stimulus / potassium channel activator activity / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / maintenance of protein location in mitochondrion / negative regulation of lymphocyte migration / cellular response to decreased oxygen levels / regulation of type B pancreatic cell development / AKT-mediated inactivation of FOXO1A / maternal placenta development / Negative regulation of the PI3K/AKT network / negative regulation of long-chain fatty acid import across plasma membrane / establishment of protein localization to mitochondrion / negative regulation of fatty acid beta-oxidation / AKT phosphorylates targets in the nucleus / regulation of glycogen biosynthetic process / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cilium assembly / positive regulation of I-kappaB phosphorylation / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / response to fluid shear stress / RUNX2 regulates genes involved in cell migration / positive regulation of organ growth / MTOR signalling / fibroblast migration / interleukin-18-mediated signaling pathway / positive regulation of sodium ion transport / mammary gland epithelial cell differentiation / negative regulation of endopeptidase activity / negative regulation of protein serine/threonine kinase activity / RAB GEFs exchange GTP for GDP on RABs / positive regulation of glucose metabolic process / positive regulation of endodeoxyribonuclease activity / response to growth factor / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of protein localization to cell surface / protein serine/threonine kinase inhibitor activity / negative regulation of leukocyte cell-cell adhesion / phosphatidylinositol-3,4-bisphosphate binding / peripheral nervous system myelin maintenance / sphingosine-1-phosphate receptor signaling pathway / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / response to growth hormone / anoikis / glycogen biosynthetic process / AKT phosphorylates targets in the cytosol / labyrinthine layer blood vessel development / execution phase of apoptosis / response to food / response to UV-A / regulation of myelination / regulation of postsynapse organization / regulation of neuron projection development / KSRP (KHSRP) binds and destabilizes mRNA / Regulation of TP53 Activity through Association with Co-factors / mammalian oogenesis stage / negative regulation of macroautophagy / CTLA4 inhibitory signaling / negative regulation of cGAS/STING signaling pathway / activation-induced cell death of T cells / negative regulation of Notch signaling pathway / behavioral response to pain / non-canonical NF-kappaB signal transduction / negative regulation of release of cytochrome c from mitochondria / Constitutive Signaling by AKT1 E17K in Cancer / apoptotic mitochondrial changes / CD28 dependent PI3K/Akt signaling / phosphatidylinositol-3,4,5-trisphosphate binding / Regulation of localization of FOXO transcription factors / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of glycogen biosynthetic process / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / TOR signaling / Activation of BAD and translocation to mitochondria / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / positive regulation of fat cell differentiation / canonical NF-kappaB signal transduction / positive regulation of G1/S transition of mitotic cell cycle / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / eNOS activation / positive regulation of lipid biosynthetic process / Cyclin E associated events during G1/S transition / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Cyclin A:Cdk2-associated events at S phase entry / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / lipopolysaccharide-mediated signaling pathway / regulation of cell migration / negative regulation of protein ubiquitination / cellular response to epidermal growth factor stimulus / 14-3-3 protein binding / Regulation of TP53 Activity through Acetylation / positive regulation of TORC1 signaling / positive regulation of endothelial cell proliferation / striated muscle cell differentiation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.4 Å | ||||||
Authors | Thomas, C.C. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
Citation | Journal: Curr.Biol. / Year: 2002 Title: High Resolution Structure of the Pleckstrin Homology Domain of Protein Kinase B/Akt Bound to Phosphatidylinositol (3,4,5)-Trisphosphate Authors: Thomas, C.C. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h10.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h10.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 1h10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h10_validation.pdf.gz | 856.4 KB | Display | wwPDB validaton report |
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Full document | 1h10_full_validation.pdf.gz | 857.9 KB | Display | |
Data in XML | 1h10_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1h10_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/1h10 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/1h10 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14940.391 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 1-123 Source method: isolated from a genetically manipulated source Details: BOUND TO INS(1,3,4,5)-TETRAKISPHOPHATE, SELENOMETHIONINE DERIVATIVE Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P31749, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical | ChemComp-4IP / |
#3: Water | ChemComp-HOH / |
Compound details | GENERAL PROTEIN KINASE, PHOSPHORYL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.07 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.2 Details: 0.25M AMMONIUM ACETATE, 30% PEG 4000,0.1M SODIUM ACETATE (PH 4.6) | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9786 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 15, 2002 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→15 Å / Num. obs: 21933 / % possible obs: 97.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 6.7 / % possible all: 83.3 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 15 Å / Redundancy: 3.8 % / Num. measured all: 83520 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS Highest resolution: 1.4 Å / % possible obs: 83.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 6.7 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 1.4→15 Å / Num. parameters: 11393 / Num. restraintsaints: 10950 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: REFINEMENT USING CNS AND THEN SHELXL -97
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Refine analyze | Occupancy sum hydrogen: 943 / Occupancy sum non hydrogen: 1249.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→15 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.125 / Rfactor Rfree: 0.175 / Rfactor Rwork: 0.125 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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