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Yorodumi- PDB-5ixi: Structure of human JAK1 FERM/SH2 in complex with IFNLR1/IL10RA chimera -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ixi | ||||||
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Title | Structure of human JAK1 FERM/SH2 in complex with IFNLR1/IL10RA chimera | ||||||
Components |
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Keywords | CYTOKINE / JAK kinase / JAK1 / IFNLR1 / IL10 / IL10RA / interferon | ||||||
Function / homology | Function and homology information interleukin-10 binding / response to type III interferon / interleukin-10 receptor activity / interleukin-28 receptor complex / mucosal immune response / ubiquitin-dependent endocytosis / intestinal epithelial structure maintenance / protein localization to cell-cell junction / positive regulation of cellular respiration / interleukin-11-mediated signaling pathway ...interleukin-10 binding / response to type III interferon / interleukin-10 receptor activity / interleukin-28 receptor complex / mucosal immune response / ubiquitin-dependent endocytosis / intestinal epithelial structure maintenance / protein localization to cell-cell junction / positive regulation of cellular respiration / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / type III interferon-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of homotypic cell-cell adhesion / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / regulation of defense response to virus by host / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / Interleukin-12 signaling / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-2 signaling / growth hormone receptor binding / cytokine receptor activity / Other interleukin signaling / IFNG signaling activates MAPKs / Interleukin-20 family signaling / regulation of synapse organization / interleukin-6-mediated signaling pathway / type I interferon-mediated signaling pathway / Interleukin-6 signaling / positive regulation of sprouting angiogenesis / MAPK3 (ERK1) activation / Interleukin-10 signaling / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / Signaling by CSF3 (G-CSF) / extrinsic component of cytoplasmic side of plasma membrane / Interleukin-7 signaling / negative regulation of autophagy / Evasion by RSV of host interferon responses / non-specific protein-tyrosine kinase / positive regulation of receptor signaling pathway via JAK-STAT / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / ISG15 antiviral mechanism / cellular response to virus / cytokine-mediated signaling pathway / negative regulation of inflammatory response / positive regulation of protein localization to nucleus / Interferon gamma signaling / Interferon alpha/beta signaling / signaling receptor activity / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / defense response to virus / Potential therapeutics for SARS / response to lipopolysaccharide / cell differentiation / cytoskeleton / endosome / intracellular signal transduction / apical plasma membrane / negative regulation of cell population proliferation / protein phosphorylation / response to antibiotic / focal adhesion / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP binding / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | ||||||
Authors | Ferrao, R. / Wallweber, H.J.A. / Lupardus, P.J. | ||||||
Citation | Journal: Structure / Year: 2016 Title: The Structural Basis for Class II Cytokine Receptor Recognition by JAK1. Authors: Ferrao, R. / Wallweber, H.J. / Ho, H. / Tam, C. / Franke, Y. / Quinn, J. / 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 | 5ixi.cif.gz | 209.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ixi.ent.gz | 164.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ixi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/5ixi ftp://data.pdbj.org/pub/pdb/validation_reports/ix/5ixi | HTTPS FTP |
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-Related structure data
Related structure data | 5ixdSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 63362.254 Da / Num. of mol.: 1 / Fragment: UNP residues 35-559 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JAK1, JAK1A, JAK1B / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P23458, non-specific protein-tyrosine kinase |
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#2: Protein | Mass: 6136.144 Da / Num. of mol.: 1 / Fragment: UNP residues 250-259,UNP residues 263-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFNLR1, IL28RA, LICR2, IL10RA, IL10R / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IU57, UniProt: Q13651 |
#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: 3.03 Å3/Da / Density % sol: 59.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES pH6.5, 0.2M MgCl2, 9% PEG4K, 25% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→36.15 Å / Num. obs: 26423 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 50.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.57→2.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2.2 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IXD Resolution: 2.57→36.15 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.57→36.15 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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