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- PDB-3ciy: Mouse Toll-like receptor 3 ectodomain complexed with double-stran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ciy | |||||||||
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Title | Mouse Toll-like receptor 3 ectodomain complexed with double-stranded RNA | |||||||||
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![]() | IMMUNE SYSTEM/RNA / Leucine Rich Repeat / LRR / protein-dsRNA complex / innate immunity / TLR / dsRNA / Glycoprotein / Immune response / Inflammatory response / Leucine-rich repeat / Membrane / Receptor / Transmembrane / IMMUNE SYSTEM-RNA COMPLEX | |||||||||
Function / homology | ![]() type III interferon production / positive regulation of type III interferon production / response to dsRNA / regulation of dendritic cell cytokine production / inflammatory response to wounding / toll-like receptor 3 signaling pathway / necroptotic signaling pathway / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage cytokine production / pattern recognition receptor activity ...type III interferon production / positive regulation of type III interferon production / response to dsRNA / regulation of dendritic cell cytokine production / inflammatory response to wounding / toll-like receptor 3 signaling pathway / necroptotic signaling pathway / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / cellular response to exogenous dsRNA / response to exogenous dsRNA / positive regulation of type I interferon production / cellular response to interferon-beta / positive regulation of interferon-alpha production / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / JNK cascade / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / response to virus / cellular response to virus / defense response / cellular response to type II interferon / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / transmembrane signaling receptor activity / positive regulation of angiogenesis / male gonad development / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / MAPK cascade / positive regulation of type II interferon production / double-stranded RNA binding / cellular response to xenobiotic stimulus / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / early endosome / endosome membrane / inflammatory response / positive regulation of apoptotic process / innate immune response / endoplasmic reticulum membrane / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liu, L. / Botos, I. / Wang, Y. / Leonard, J.N. / Shiloach, J. / Segal, D.M. / Davies, D.R. | |||||||||
![]() | ![]() Title: Structural basis of toll-like receptor 3 signaling with double-stranded RNA. Authors: Liu, L. / Botos, I. / Wang, Y. / Leonard, J.N. / Shiloach, J. / Segal, D.M. / Davies, D.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 341.5 KB | Display | ![]() |
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PDB format | ![]() | 267.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.3 MB | Display | ![]() |
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Full document | ![]() | 4.4 MB | Display | |
Data in XML | ![]() | 66.1 KB | Display | |
Data in CIF | ![]() | 91.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cigSC S: Starting model for refinement C: citing same article ( |
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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
-RNA chain , 2 types, 2 molecules CD
#1: RNA chain | Mass: 14781.812 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Most of the sequence occurs naturally in West Nile Virus |
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#2: RNA chain | Mass: 14655.683 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Most of the sequence occurs naturally in West Nile Virus |
-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 79631.320 Da / Num. of mol.: 2 / Fragment: mouse TLR3 ectodomain (UNP residues 28-704) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 10 types, 18 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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 | 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 #7: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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 #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: 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 #11: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #12: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #13: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.58 Å3/Da / Density % sol: 73.12 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 13% PEG 3350, 5% Dextran 5000, 0.2M Ammonium Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 70 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2007 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. all: 47483 / Num. obs: 46438 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 1.81 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CIG Resolution: 3.41→47.29 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 8057301.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 78.7161 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 154.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.41→47.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.61 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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