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Open data
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Basic information
Entry | Database: PDB / ID: 3wo4 | |||||||||
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Title | Crystal structure of the IL-18 signaling ternary complex | |||||||||
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![]() | IMMUNE SYSTEM / ternary complex / beta trefoil fold (ligand) / three immunoglobulin-like domains (receptors) / immunity / inflammation / autoimmunity / allergy / glycosylation / serum / membrane | |||||||||
Function / homology | ![]() 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 / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / natural killer cell mediated cytotoxicity / negative regulation of myoblast differentiation / type 2 immune response / natural killer cell activation / sleep / neutrophil activation / 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 / positive regulation of natural killer cell proliferation / negative regulation of cold-induced thermogenesis / 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 / coreceptor activity / 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 / cellular response to hydrogen peroxide / 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 / cellular response to lipopolysaccharide / angiogenesis / Interleukin-4 and Interleukin-13 signaling / 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tsutsumi, N. / Kimura, T. / Arita, K. / Ariyoshi, M. / Ohnishi, H. / Kondo, N. / Shirakawa, M. / Kato, Z. / Tochio, H. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 324.5 KB | Display | ![]() |
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PDB format | ![]() | 263 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 38.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wo2C ![]() 3wo3SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18239.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Interleukin-18 receptor ... , 2 types, 2 molecules BC
#2: Protein | Mass: 35899.738 Da / Num. of mol.: 1 / Fragment: UNP residues 20-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Protein | Mass: 39235.637 Da / Num. of mol.: 1 / Fragment: UNP residues 15-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 7 types, 10 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...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 | ||||||
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#5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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 | ||||||
#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 | Source method: isolated from a genetically manipulated source #8: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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 #9: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 #10: Sugar | |
-Non-polymers , 2 types, 32 molecules ![](data/chem/img/CL.gif)
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#11: Chemical | ChemComp-CL / |
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#12: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 100mM Tris-HCl, 18% polyethylene glycol 4000, 200mM magnesium chloride, 40mM hexaamminecobalt (III) chloride, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 21, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 20680 / Num. obs: 20659 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 60.09 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2029 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WO3 Resolution: 3.1→42 Å / Cor.coef. Fo:Fc: 0.9234 / Cor.coef. Fo:Fc free: 0.8813 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.441 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 188.95 Å2 / Biso mean: 77.81 Å2 / Biso min: 8.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.616 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Total num. of bins used: 9
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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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