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Yorodumi- PDB-3wpe: Crystal structure of bovine TLR9 in complex with agonistic DNA166... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wpe | ||||||
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Title | Crystal structure of bovine TLR9 in complex with agonistic DNA1668_12mer | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Leucine rich repeat / Receptor / Innate immunity / DNA binding / Glycosylation / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information 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 / early phagosome / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interferon-alpha production ...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 / early phagosome / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interferon-alpha production / positive regulation of immunoglobulin production / canonical NF-kappaB signal transduction / positive regulation of B cell proliferation / activation of innate immune response / positive regulation of interferon-beta production / 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 / endosome / inflammatory response / innate immune response / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) synthetic (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Ohto, U. / Tanji, H. / Shimizu, T. | ||||||
Citation | Journal: Nature / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wpe.cif.gz | 282.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wpe.ent.gz | 237.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wpe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/3wpe ftp://data.pdbj.org/pub/pdb/validation_reports/wp/3wpe | HTTPS FTP |
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-Related structure data
Related structure data | 3wpbC 3wpcC 3wpdC 3wpfC 3wpgC 3wphC 3wpiC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 89323.531 Da / Num. of mol.: 1 / Fragment: Extracellular domain, UNP residues 25-815 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: TLR9 / Cell (production host): SCHNEIDER 2(S2) / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q5I2M5 |
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#2: DNA chain | Mass: 3613.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 3-5% PEG 4000, 0.2M Na acetate, 0.1M Na citrate pH 5.5, 15% DMSO , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
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: 2.38→48.11 Å / Num. obs: 34012 / Rmerge(I) obs: 0.113 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→43.05 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.895 / SU B: 21.279 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.281 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.268 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→43.05 Å
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