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Open data
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Basic information
Entry | Database: PDB / ID: 3wpb | |||||||||
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Title | Crystal structure of horse TLR9 (unliganded form) | |||||||||
![]() | Toll-like receptor 9 | |||||||||
![]() | DNA BINDING PROTEIN / Leucine rich repeat / Receptor / Innate immunity / DNA binding / Glycosylation / CpG motif | |||||||||
Function / homology | ![]() regulation of B cell differentiation / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of B cell activation / unmethylated CpG binding / siRNA binding / pattern recognition receptor activity / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / canonical NF-kappaB signal transduction ...regulation of B cell differentiation / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of B cell activation / unmethylated CpG binding / siRNA binding / pattern recognition receptor activity / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / positive regulation of B cell proliferation / activation of innate immune response / positive regulation of interferon-beta production / phagocytic vesicle / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of NF-kappaB transcription factor activity / defense response to virus / positive regulation of MAPK cascade / lysosome / inflammatory response / innate immune response / endoplasmic reticulum membrane / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ohto, U. / Tanji, H. / Shimizu, T. | |||||||||
![]() | ![]() Title: Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9 Authors: Ohto, U. / Shibata, T. / Tanji, H. / Ishida, H. / Krayukhina, E. / Uchiyama, S. / Miyake, K. / Shimizu, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 287.2 KB | Display | ![]() |
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PDB format | ![]() | 233.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 772.5 KB | Display | ![]() |
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Full document | ![]() | 776.3 KB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 39.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wpcC ![]() 3wpdC ![]() 3wpeC ![]() 3wpfC ![]() 3wpgC ![]() 3wphC ![]() 3wpiC 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
#1: Protein | Mass: 89427.562 Da / Num. of mol.: 1 / Fragment: UNP residues 26-817 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: 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 | ||||
#3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 14-10% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Na acetate pH 4.5, 10% ethylene glycol , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→36.85 Å / Num. obs: 31314 / Rsym value: 0.162 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.015 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→36.85 Å
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Refine LS restraints |
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