[English] 日本語
![](img/lk-miru.gif)
- PDB-3wpe: Crystal structure of bovine TLR9 in complex with agonistic DNA166... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3wpe | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of bovine TLR9 in complex with agonistic DNA1668_12mer | ||||||
![]() |
| ||||||
![]() | DNA BINDING PROTEIN/DNA / Leucine rich repeat / Receptor / Innate immunity / DNA binding / Glycosylation / DNA BINDING PROTEIN-DNA complex | ||||||
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 / early phagosome / pattern recognition receptor activity / positive regulation of immunoglobulin production / toll-like receptor signaling pathway ...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 / 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 / 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 | ![]() ![]() synthetic (others) | ||||||
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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 282.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 237.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 446.6 KB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wpbC ![]() 3wpcC ![]() 3wpdC ![]() 3wpfC ![]() 3wpgC ![]() 3wphC ![]() 3wpiC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() ![]() |
---|---|
#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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.32 % |
---|---|
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 |
---|---|
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: 2.38→48.11 Å / Num. obs: 34012 / Rmerge(I) obs: 0.113 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→43.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|