+Open data
-Basic information
Entry | Database: PDB / ID: 5zsl | |||||||||
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Title | Crystal structure of monkey TLR7 in complex with GGUUGG | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Innate immunity Toll-like receptors | |||||||||
Function / homology | Function and homology information toll-like receptor 7 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / positive regulation of chemokine production ...toll-like receptor 7 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / positive regulation of chemokine production / JNK cascade / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / regulation of protein phosphorylation / cellular response to virus / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / positive regulation of type II interferon production / double-stranded RNA binding / defense response to virus / single-stranded RNA binding / receptor complex / lysosome / endosome / inflammatory response / innate immune response / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Macaca mulatta (Rhesus monkey) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | |||||||||
Authors | Zhang, Z. / Ohto, U. / Shimizu, T. | |||||||||
Citation | Journal: Cell Rep / Year: 2018 Title: Structural Analyses of Toll-like Receptor 7 Reveal Detailed RNA Sequence Specificity and Recognition Mechanism of Agonistic Ligands. Authors: Zhang, Z. / Ohto, U. / Shibata, T. / Taoka, M. / Yamauchi, Y. / Sato, R. / Shukla, N.M. / David, S.A. / Isobe, T. / 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 | 5zsl.cif.gz | 336.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zsl.ent.gz | 265.8 KB | Display | PDB format |
PDBx/mmJSON format | 5zsl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/5zsl ftp://data.pdbj.org/pub/pdb/validation_reports/zs/5zsl | HTTPS FTP |
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-Related structure data
Related structure data | 5zsaC 5zsbC 5zscC 5zsdC 5zseC 5zsfC 5zsgC 5zshC 5zsiC 5zsjC 5zsmC 5zsnC 6if5C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 27 - 835 / Label seq-ID: 5 - 813
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-Components
-Protein / RNA chain , 2 types, 4 molecules BADE
#1: Protein | Mass: 94745.594 Da / Num. of mol.: 2 / Fragment: UNP residues 27-839 / Mutation: N167Q,N389Q,N488Q,N799Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: TLR7 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: B3Y653 #2: RNA chain | Mass: 1932.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Sugars , 2 types, 15 molecules
#3: 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 #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 24 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | The residues 440-445 (SEVGFC) are replaced by a thrombin-cleavage sequence (LVPRGS) for artificial ...The residues 440-445 (SEVGFC) are replaced by a thrombin-cleavage sequence (LVPRGS) for artificial cleavage of Z-loop. This engineered site in Z-loop was further cleaved during purification and the cleaved protein remained associated via interactions between LRRs and a disulfide bond. Therefore, although cleaved, the cleaved version of protein is considered as one single component (chain). |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEG 8000, ammonium sulfate, sodium citrate pH 5.0, Tris-HCl pH 7.5 and NaCl |
-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: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 93814 / % possible obs: 99.9 % / Redundancy: 6.7 % / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.3→2.34 Å |
-Processing
Software |
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Refinement | Resolution: 2.3→47.36 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.159 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.231 / 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: 50.597 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→47.36 Å
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