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Yorodumi- PDB-3bu3: Crystal structure of the insulin receptor kinase in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 3bu3 | ||||||
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Title | Crystal structure of the insulin receptor kinase in complex with IRS2 KRLB peptide | ||||||
Components |
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Keywords | TRANSFERASE / IRK / KRLB / IRS2 / insulin receptor / substrate / Alternative splicing / ATP-binding / Carbohydrate metabolism / Cleavage on pair of basic residues / Diabetes mellitus / Disease mutation / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / Transmembrane / Tyrosine-protein kinase / Transducer | ||||||
Function / homology | Function and homology information IRS-mediated signalling / IRS-related events triggered by IGF1R / Signaling by Erythropoietin / positive regulation of type B pancreatic cell proliferation / SOS-mediated signalling / PI3K/AKT activation / Erythropoietin activates RAS / PI3K Cascade / IRS activation / Interleukin-7 signaling ...IRS-mediated signalling / IRS-related events triggered by IGF1R / Signaling by Erythropoietin / positive regulation of type B pancreatic cell proliferation / SOS-mediated signalling / PI3K/AKT activation / Erythropoietin activates RAS / PI3K Cascade / IRS activation / Interleukin-7 signaling / Signal attenuation / epithelial cell migration / negative regulation of long-chain fatty acid import across plasma membrane / RAF/MAP kinase cascade / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PIP3 activates AKT signaling / regulation of female gonad development / positive regulation of meiotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of developmental growth / positive regulation of fatty acid beta-oxidation / phosphatidylinositol 3-kinase activator activity / insulin-like growth factor II binding / RET signaling / type B pancreatic cell proliferation / male sex determination / exocrine pancreas development / mammary gland development / insulin receptor complex / insulin-like growth factor I binding / positive regulation of glucose metabolic process / insulin receptor activity / transmembrane receptor protein tyrosine kinase adaptor activity / negative regulation of B cell apoptotic process / positive regulation of protein-containing complex disassembly / cargo receptor activity / positive regulation of mesenchymal cell proliferation / dendritic spine maintenance / insulin binding / PTB domain binding / negative regulation of kinase activity / neuronal cell body membrane / adrenal gland development / Signaling by Insulin receptor / IRS activation / positive regulation of epithelial cell migration / amyloid-beta clearance / activation of protein kinase activity / positive regulation of respiratory burst / regulation of embryonic development / positive regulation of receptor internalization / transport across blood-brain barrier / insulin receptor substrate binding / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / response to glucose / phosphatidylinositol 3-kinase binding / heart morphogenesis / positive regulation of B cell proliferation / dendrite membrane / Insulin receptor recycling / insulin-like growth factor receptor binding / receptor-mediated endocytosis / neuron projection maintenance / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / 14-3-3 protein binding / learning / caveola / cellular response to glucose stimulus / positive regulation of glucose import / brain development / positive regulation of MAP kinase activity / insulin receptor binding / receptor internalization / positive regulation of insulin secretion / receptor protein-tyrosine kinase / memory / cellular response to growth factor stimulus / peptidyl-tyrosine phosphorylation / cellular response to insulin stimulus / male gonad development / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of nitric oxide biosynthetic process / cell migration / protein-macromolecule adaptor activity / late endosome / glucose homeostasis / insulin receptor signaling pathway / amyloid-beta binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein phosphatase binding / protein tyrosine kinase activity / cell population proliferation / positive regulation of MAPK cascade / protein autophosphorylation / lysosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Wu, J. / Hubbard, S.R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Structural and biochemical characterization of the KRLB region in insulin receptor substrate-2. Authors: Wu, J. / Tseng, Y.D. / Xu, C.F. / Neubert, T.A. / White, M.F. / Hubbard, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bu3.cif.gz | 77 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bu3.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/3bu3 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3bu3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35033.660 Da / Num. of mol.: 1 / Fragment: protein kinase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 References: UniProt: P06213, receptor protein-tyrosine kinase |
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#2: Protein/peptide | Mass: 1715.769 Da / Num. of mol.: 1 / Fragment: UNP residues 620-634 / Source method: obtained synthetically Details: The sequence of this peptide natually exists in Mus Musculus. References: UniProt: P81122 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28% PEG8000 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A |
Detector | Detector: CCD / Date: Apr 4, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 43554 / Num. obs: 41344 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.8 / Num. unique all: 43554 / Rsym value: 0.347 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→46.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.98 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.101 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→46.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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