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Yorodumi- PDB-2b4s: Crystal structure of a complex between PTP1B and the insulin rece... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b4s | ||||||
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Title | Crystal structure of a complex between PTP1B and the insulin receptor tyrosine kinase | ||||||
Components |
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Keywords | Hydrolase/transferase / phosphorylation / tyrosine protein kinase / Hydrolase-transferase complex | ||||||
Function / homology | Function and homology information regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly ...regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly / cargo receptor activity / dendritic spine maintenance / insulin binding / PTB domain binding / adrenal gland development / regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / positive regulation of receptor catabolic process / insulin receptor recycling / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / Signaling by Insulin receptor / IRS activation / activation of protein kinase activity / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / neuronal cell body membrane / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / amyloid-beta clearance / positive regulation of respiratory burst / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / positive regulation of receptor internalization / regulation of embryonic development / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / insulin receptor substrate binding / transport across blood-brain barrier / Regulation of IFNA/IFNB signaling / positive regulation of glycogen biosynthetic process / regulation of signal transduction / epidermis development / cellular response to unfolded protein / growth hormone receptor signaling pathway via JAK-STAT / Signal attenuation / phosphatidylinositol 3-kinase binding / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / heart morphogenesis / MECP2 regulates neuronal receptors and channels / Growth hormone receptor signaling / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / insulin-like growth factor receptor binding / dendrite membrane / neuron projection maintenance / ephrin receptor binding / activation of protein kinase B activity / positive regulation of glycolytic process / Integrin signaling / protein dephosphorylation / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / protein-tyrosine-phosphatase / receptor-mediated endocytosis / negative regulation of MAP kinase activity / protein phosphatase 2A binding / learning / protein tyrosine phosphatase activity / caveola / endosome lumen / positive regulation of glucose import / positive regulation of MAP kinase activity / insulin receptor binding / Negative regulation of MET activity / receptor protein-tyrosine kinase / receptor internalization / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / memory / cellular response to growth factor stimulus / peptidyl-tyrosine phosphorylation / cellular response to insulin stimulus / male gonad development / positive regulation of nitric oxide biosynthetic process / late endosome / insulin receptor signaling pathway / glucose homeostasis / amyloid-beta binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / actin cytoskeleton organization Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Li, S. / Depetris, R.S. / Barford, D. / Chernoff, J. / Hubbard, S.R. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Crystal Structure of a Complex between Protein Tyrosine Phosphatase 1B and the Insulin Receptor Tyrosine Kinase. Authors: Li, S. / Depetris, R.S. / Barford, D. / Chernoff, J. / 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 | 2b4s.cif.gz | 247.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b4s.ent.gz | 196.5 KB | Display | PDB format |
PDBx/mmJSON format | 2b4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/2b4s ftp://data.pdbj.org/pub/pdb/validation_reports/b4/2b4s | 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: 34688.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase #2: Protein | Mass: 35033.660 Da / Num. of mol.: 2 / 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, EC: 2.7.1.112 #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Tris-HCl, 1.9 M ammonium sulfate, 2% PEG 400, pH 7.5, temperature 277K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Detector: CCD / Date: Apr 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 61660 / Num. obs: 60480 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.104 |
Reflection shell | Resolution: 2.3→2.37 Å / Rmerge(I) obs: 0.272 / % possible all: 94.2 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IR3, 1G1H Resolution: 2.3→29.49 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 175542.24 / Data cutoff high rms absF: 175542.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.272 Å2 / ksol: 0.357338 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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