+Open data
-Basic information
Entry | Database: PDB / ID: 3wo3 | |||||||||
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Title | Crystal structure of IL-18 in complex with IL-18 receptor alpha | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / binary complex / beta trefoil fold (ligand) / three immunoglobulin-like domains (receptor) / immunity / inflammation / autoimmunity / allergy / interleukin-18 receptor beta / glycosylation / serum / membrane | |||||||||
Function / homology | Function and homology information interleukin-18 binding / interleukin-18 receptor activity / interleukin-18 receptor complex / interleukin-18 receptor binding / interleukin-1 receptor activity / T-helper 1 cell differentiation / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production ...interleukin-18 binding / interleukin-18 receptor activity / interleukin-18 receptor complex / interleukin-18 receptor binding / interleukin-1 receptor activity / T-helper 1 cell differentiation / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation / NAD+ nucleosidase activity / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / positive regulation of interleukin-13 production / natural killer cell mediated cytotoxicity / negative regulation of myoblast differentiation / type 2 immune response / natural killer cell activation / neutrophil activation / sleep / NAD+ nucleotidase, cyclic ADP-ribose generating / Interleukin-1 processing / positive regulation of NK T cell proliferation / Interleukin-37 signaling / triglyceride homeostasis / positive regulation of granulocyte macrophage colony-stimulating factor production / negative regulation of cold-induced thermogenesis / positive regulation of natural killer cell proliferation / T-helper 1 type immune response / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / establishment of skin barrier / Pyroptosis / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / cholesterol homeostasis / positive regulation of smooth muscle cell proliferation / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / cell-cell signaling / signaling receptor activity / positive regulation of cold-induced thermogenesis / positive regulation of NF-kappaB transcription factor activity / Interleukin-4 and Interleukin-13 signaling / angiogenesis / cellular response to lipopolysaccharide / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / inflammatory response / immune response / signal transduction / 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: 3.1 Å | |||||||||
Authors | Tsutsumi, N. / Kimura, T. / Arita, K. / Ariyoshi, M. / Ohnishi, H. / Kondo, N. / Shirakawa, M. / Kato, Z. / Tochio, H. | |||||||||
Citation | Journal: Nat Commun / Year: 2014 Title: The structural basis for receptor recognition of human interleukin-18 Authors: Tsutsumi, N. / Kimura, T. / Arita, K. / Ariyoshi, M. / Ohnishi, H. / Yamamoto, T. / Zuo, X. / Maenaka, K. / Park, E.Y. / Kondo, N. / Shirakawa, M. / Tochio, H. / Kato, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wo3.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3wo3.ent.gz | 940.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/3wo3 ftp://data.pdbj.org/pub/pdb/validation_reports/wo/3wo3 | HTTPS FTP |
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-Related structure data
Related structure data | 3wo2C 3wo4C 3f62S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein | Mass: 18239.727 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14116 #2: Protein | Mass: 35899.738 Da / Num. of mol.: 6 / Fragment: UNP residues 20-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL18R1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13478 |
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-Sugars , 10 types, 34 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #11: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #13: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 137 molecules
#12: Chemical | ChemComp-SO4 / #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 50mM N-Cyclohexyl-3-aminopropanesulfonic acid, 35% pentaerythritol ethoxylate (15/4 EO/OH), 350mM ammonium sulfate, 50mM LysoFos Choline 10, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 6, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→43.93 Å / Num. all: 79498 / Num. obs: 79180 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 85.33 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11521 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F62 Resolution: 3.1→31.25 Å / Cor.coef. Fo:Fc: 0.9149 / Cor.coef. Fo:Fc free: 0.8855 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.355 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 208.32 Å2 / Biso mean: 81.11 Å2 / Biso min: 17.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.578 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→31.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 20
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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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