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Yorodumi- PDB-4po6: Crystal structure of the human TYK2 FERM and SH2 domains with an ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4po6 | ||||||
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Title | Crystal structure of the human TYK2 FERM and SH2 domains with an IFNAR1 intracellular peptide | ||||||
Components |
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Keywords | TRANSFERASE / FERM / SH2 / kinase / receptor / cytokine / intracellular | ||||||
Function / homology | Function and homology information type I interferon receptor activity / type I interferon binding / JAK pathway signal transduction adaptor activity / cellular response to interferon-alpha / positive regulation of cellular respiration / type III interferon-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response ...type I interferon receptor activity / type I interferon binding / JAK pathway signal transduction adaptor activity / cellular response to interferon-alpha / positive regulation of cellular respiration / type III interferon-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / type 1 angiotensin receptor binding / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / Interleukin-12 signaling / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / growth hormone receptor binding / Other interleukin signaling / extrinsic component of plasma membrane / Interleukin-20 family signaling / Interleukin-6 signaling / type I interferon-mediated signaling pathway / cytokine binding / positive regulation of interleukin-17 production / MAPK3 (ERK1) activation / Interleukin-10 signaling / MAPK1 (ERK2) activation / positive regulation of natural killer cell proliferation / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta / growth hormone receptor signaling pathway via JAK-STAT / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / positive regulation of T cell proliferation / non-specific protein-tyrosine kinase / positive regulation of receptor signaling pathway via JAK-STAT / response to virus / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / 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 / late endosome / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / response to lipopolysaccharide / cell differentiation / lysosome / cytoskeleton / intracellular signal transduction / immune response / protein phosphorylation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular exosome / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å | ||||||
Authors | Wallweber, H.J.A. / Lupardus, P.J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 Title: Structural basis of IFN receptor recognition by TYK2 Authors: Wallweber, H.J.A. / Tam, C. / Franke, Y. / Starovasnik, M.A. / Lupardus, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4po6.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4po6.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 4po6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/4po6 ftp://data.pdbj.org/pub/pdb/validation_reports/po/4po6 | HTTPS FTP |
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-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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Details | single TYK2/IFNAR1 complex in assymetric unit |
-Components
#1: Protein | Mass: 63598.633 Da / Num. of mol.: 1 / Fragment: unp residues 23-583 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYK2 / Plasmid: pAC / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P29597, non-specific protein-tyrosine kinase | ||
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#2: Protein/peptide | Mass: 3864.246 Da / Num. of mol.: 1 / Fragment: unp residues 475-507 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR, IFNAR1 / Plasmid: pAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17181 | ||
#3: Chemical | #4: 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: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 293 K / pH: 7 Details: 0.1 M Tris HCl pH 7.0, 0.2 M MgCl2, and 8-12% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→38.55 Å / Num. obs: 42667 / % possible obs: 96.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.04 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.99→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.2 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: SAD MODEL Resolution: 1.99→38.55 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.895 / SU R Cruickshank DPI: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 50.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.289 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→38.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.04 Å / Total num. of bins used: 20
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