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Open data
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Basic information
Entry | Database: PDB / ID: 3cig | |||||||||
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Title | Crystal structure of mouse TLR3 ectodomain | |||||||||
![]() | Toll-like receptor 3 | |||||||||
![]() | IMMUNE SYSTEM / leucine-rich repeat / innate immunity / TLR / LRR / Glycoprotein / Immune response / Inflammatory response / Membrane / Receptor / Transmembrane | |||||||||
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 | ![]() | 158.6 KB | Display | ![]() |
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PDB format | ![]() | 122.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 44.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ciyC ![]() 2a0zS 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 / Non-polymers , 2 types, 80 molecules A![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: Protein | Mass: 79631.320 Da / Num. of mol.: 1 / Fragment: mouse TLR3 ectodomain (UNP residues 28-704) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#9: Water | ChemComp-HOH / |
-Sugars , 7 types, 12 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/FUC.gif)
![](data/chem/img/FUC.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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 #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-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 #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / #8: Sugar | ChemComp-FUC / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.63 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 15% PEG 6000, 5% dextran 5000, 1M lithium chloride, 0.1M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-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: 2.7→50 Å / Num. all: 34817 / Num. obs: 33494 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.125 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 1.79 / Num. unique all: 3391 / % possible all: 90.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 2a0z Resolution: 2.66→50 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.879 / SU B: 28.948 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.541 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.685 Å2
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Refinement step | Cycle: LAST / Resolution: 2.66→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.663→2.732 Å / Total num. of bins used: 20
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