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Yorodumi- PDB-8exn: Crystal structure of PTP1B D181A/Q262A phosphatase domain with TY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8exn | ||||||
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Title | Crystal structure of PTP1B D181A/Q262A phosphatase domain with TYK2 activation loop phosphopeptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / PTP1B / JAK/STAT / IRK | ||||||
Function / homology | Function and homology information type III interferon-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / type 1 angiotensin receptor binding / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / Interleukin-12 signaling / Interleukin-27 signaling ...type III interferon-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / type 1 angiotensin receptor binding / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / Interleukin-12 signaling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-35 Signalling / positive regulation of natural killer cell proliferation / growth hormone receptor binding / Other interleukin signaling / regulation of hepatocyte growth factor receptor signaling pathway / extrinsic component of plasma membrane / PTK6 Down-Regulation / Interleukin-20 family signaling / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / type I interferon-mediated signaling pathway / Interleukin-6 signaling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / MAPK3 (ERK1) activation / positive regulation of interleukin-17 production / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / Interleukin-10 signaling / positive regulation of IRE1-mediated unfolded protein response / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / type II interferon-mediated signaling pathway / MECP2 regulates neuronal receptors and channels / Growth hormone receptor signaling / positive regulation of T cell proliferation / Signaling by CSF3 (G-CSF) / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / Insulin receptor recycling / negative regulation of insulin receptor signaling pathway / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / protein phosphatase 2A binding / protein tyrosine phosphatase activity / endosome lumen / non-specific protein-tyrosine kinase / positive regulation of receptor signaling pathway via JAK-STAT / non-membrane spanning protein tyrosine kinase activity / insulin receptor binding / Negative regulation of MET activity / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / cytoplasmic side of plasma membrane / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / Interferon alpha/beta signaling / positive regulation of type II interferon production / Signaling by ALK fusions and activated point mutants / insulin receptor signaling pathway / actin cytoskeleton organization / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / cell differentiation / early endosome / cytoskeleton / intracellular signal transduction / mitochondrial matrix / cadherin binding / immune response / protein phosphorylation / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / enzyme binding / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å | ||||||
Authors | Morris, R. / Kershaw, N.J. / Babon, J.J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Commun Biol / Year: 2023 Title: Structure guided studies of the interaction between PTP1B and JAK. Authors: Morris, R. / Keating, N. / Tan, C. / Chen, H. / Laktyushin, A. / Saiyed, T. / Liau, N.P.D. / Nicola, N.A. / Tiganis, T. / Kershaw, N.J. / Babon, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8exn.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8exn.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 8exn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8exn_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8exn_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8exn_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 8exn_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/8exn ftp://data.pdbj.org/pub/pdb/validation_reports/ex/8exn | HTTPS FTP |
-Related structure data
Related structure data | 8exiC 8exjC 8exkC 8exmC 8eyaC 8eybC 8eycC 8f88C 1sugS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34732.664 Da / Num. of mol.: 1 / Mutation: D181A/Q262A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase | ||||
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#2: Protein/peptide | Mass: 1823.894 Da / Num. of mol.: 1 / Fragment: residues 1048-1062 of TYK2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: P29597, non-specific protein-tyrosine kinase | ||||
#3: Chemical | ChemComp-PO4 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.17 % |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Calcium Acetate, 12.5% PEG 4K, 0.05 M MES (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→45.24 Å / Num. obs: 28847 / % possible obs: 99.54 % / Redundancy: 7.3 % / CC1/2: 0.99 / Net I/σ(I): 11.38 |
Reflection shell | Resolution: 2.15→2.23 Å / Num. unique obs: 2809 / CC1/2: 0.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SUG Resolution: 2.151→45.236 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.28 Å2 / Biso mean: 64.5384 Å2 / Biso min: 38.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.151→45.236 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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