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Yorodumi- PDB-1y6k: Crystal structure of human IL-10 complexed with the soluble IL-10... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y6k | ||||||
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Title | Crystal structure of human IL-10 complexed with the soluble IL-10R1 chain | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HELIX BUNDLE / RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information interleukin-10 binding / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor activity / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / negative regulation of interferon-alpha production / negative regulation of chemokine (C-C motif) ligand 5 production ...interleukin-10 binding / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor activity / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / negative regulation of interferon-alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / response to carbon monoxide / positive regulation of plasma cell differentiation / positive regulation of B cell apoptotic process / ubiquitin-dependent endocytosis / response to inactivity / chronic inflammatory response to antigenic stimulus / cytoplasmic sequestering of NF-kappaB / intestinal epithelial structure maintenance / negative regulation of membrane protein ectodomain proteolysis / regulation of isotype switching / negative regulation of heterotypic cell-cell adhesion / negative regulation of cytokine production involved in immune response / negative regulation of interleukin-1 production / negative regulation of MHC class II biosynthetic process / branching involved in labyrinthine layer morphogenesis / negative regulation of interleukin-8 production / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / type 2 immune response / endothelial cell apoptotic process / positive regulation of macrophage activation / positive regulation of MHC class II biosynthetic process / leukocyte chemotaxis / positive regulation of heterotypic cell-cell adhesion / positive regulation of signaling receptor activity / negative regulation of cytokine production / CD163 mediating an anti-inflammatory response / positive regulation of immunoglobulin production / cellular response to hepatocyte growth factor stimulus / regulation of synapse organization / positive regulation of sprouting angiogenesis / B cell proliferation / negative regulation of B cell proliferation / defense response to protozoan / negative regulation of vascular associated smooth muscle cell proliferation / Interleukin-10 signaling / negative regulation of interleukin-6 production / hemopoiesis / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of mitotic cell cycle / positive regulation of cell cycle / negative regulation of T cell proliferation / response to glucocorticoid / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / B cell differentiation / negative regulation of autophagy / FCGR3A-mediated IL10 synthesis / response to activity / positive regulation of cytokine production / cytokine activity / cellular response to estradiol stimulus / liver regeneration / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / response to insulin / Signaling by ALK fusions and activated point mutants / response to molecule of bacterial origin / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of inflammatory response / positive regulation of miRNA transcription / signaling receptor activity / regulation of gene expression / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / response to lipopolysaccharide / protein dimerization activity / defense response to bacterium / response to xenobiotic stimulus / apical plasma membrane / negative regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Yoon, S.I. / Jones, B.C. / Josepson, K. / Logsdon, N.J. / Walter, M.R. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Same structure, different function crystal structure of the Epstein-Barr virus IL-10 bound to the soluble IL-10R1 chain. Authors: Yoon, S.I. / Jones, B.C. / Logsdon, N.J. / Walter, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y6k.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y6k.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 1y6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/1y6k ftp://data.pdbj.org/pub/pdb/validation_reports/y6/1y6k | HTTPS FTP |
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-Related structure data
Related structure data | 1y6mC 1y6nC 1j7vS 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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Details | he second part of the biological assembly is generated by the two fold axis: x, x-y, -z. |
-Components
#1: Protein | Mass: 18672.447 Da / Num. of mol.: 1 / Fragment: residues 19-178 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL10 / Plasmid: pET-32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P22301 |
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#2: Protein | Mass: 24506.551 Da / Num. of mol.: 1 / Fragment: Extracellular domain, residues 22-235 / Mutation: N29Q, N53Q, N89Q, N133Q, N156Q, N168Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL10RA, IL10R / Plasmid: pMTV5HIS / Cell line (production host): SCHNEIDER CELLS / Production host: Drosophila melanogaster (fruit fly) / References: 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: 2.2 Å3/Da / Density % sol: 44.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 6000, magnesium chloride, ADA, cymal-6, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9184 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→50 Å / Num. all: 11441 / Num. obs: 11441 / % possible obs: 84.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.037 |
Reflection shell | Resolution: 2.52→2.61 Å / Rmerge(I) obs: 0.308 / % possible all: 68.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1j7V Resolution: 2.52→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.52→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.52→2.59 Å
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