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- PDB-3wph: Crystal structure of mouse TLR9 in complex with inhibitory DNA408... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wph | ||||||
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Title | Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 2) | ||||||
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![]() | DNA BINDING PROTEIN/DNA / Leucine rich repeat / Receptor / Innate immunity / DNA binding / Glycosylation / CpG motif / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() positive regulation of intestinal epithelial cell development / Toll Like Receptor 9 (TLR9) Cascade / regulation of toll-like receptor 9 signaling pathway / cellular response to chloroquine / regulation of B cell activation / Trafficking and processing of endosomal TLR / PI3K Cascade / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome ...positive regulation of intestinal epithelial cell development / Toll Like Receptor 9 (TLR9) Cascade / regulation of toll-like receptor 9 signaling pathway / cellular response to chloroquine / regulation of B cell activation / Trafficking and processing of endosomal TLR / PI3K Cascade / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome / cellular response to metal ion / regulation of dendritic cell cytokine production / positive regulation of toll-like receptor 9 signaling pathway / maintenance of gastrointestinal epithelium / positive regulation of interleukin-18 production / positive regulation of B cell activation / unmethylated CpG binding / toll-like receptor 9 signaling pathway / siRNA binding / early phagosome / interleukin-1 receptor binding / positive regulation of granulocyte macrophage colony-stimulating factor production / MyD88-dependent toll-like receptor signaling pathway / pattern recognition receptor activity / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / positive regulation of interleukin-10 production / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / positive regulation of autophagy / positive regulation of chemokine production / positive regulation of B cell proliferation / positive regulation of interleukin-12 production / activation of innate immune response / positive regulation of interferon-beta production / phagocytic vesicle / positive regulation of cytokine production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / regulation of protein phosphorylation / microglial cell activation / response to virus / response to molecule of bacterial origin / negative regulation of ERK1 and ERK2 cascade / positive regulation of non-canonical NF-kappaB signal transduction / male gonad development / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / basolateral plasma membrane / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / defense response to virus / positive regulation of MAPK cascade / lysosome / endosome / immune response / apical plasma membrane / innate immune response / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ohto, U. / 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 | ![]() | 322.1 KB | Display | ![]() |
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PDB format | ![]() | 261.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467 KB | Display | ![]() |
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Full document | ![]() | 480.2 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 40.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wpbC ![]() 3wpcC ![]() 3wpdC ![]() 3wpeC ![]() 3wpfC ![]() 3wpgC ![]() 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: 90172.562 Da / Num. of mol.: 1 / Fragment: Extracellular domain, UNP residues 26-818 / Mutation: N200Q, N242Q, N309Q, N495Q, N568Q, N695Q, N752Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: DNA chain | Mass: 3727.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others) | ||||
#3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 6-8% PEG 8000, 0.4M Ammonium sulfate, 0.1M Tris pH 8.0, 10% DMSO , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.327→57.35 Å / Num. obs: 53154 / Biso Wilson estimate: 40.27 Å2 / Rsym value: 0.084 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.36 Å2 / Biso mean: 48.7 Å2 / Biso min: 13.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.327→38.949 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Origin x: 29.2331 Å / Origin y: -0.5987 Å / Origin z: 20.8747 Å
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Refinement TLS group | Selection details: all |