+Open data
-Basic information
Entry | Database: PDB / ID: 5gmh | |||||||||
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Title | Crystal structure of monkey TLR7 in complex with R848 | |||||||||
Components | Toll-like receptor 7 | |||||||||
Keywords | IMMUNE SYSTEM / TLR7 / innate immunity / ssRNA recogniton | |||||||||
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 / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / positive regulation of interleukin-6 production / double-stranded RNA binding / positive regulation of type II interferon production / defense response to virus / single-stranded RNA binding / lysosome / receptor complex / endosome / inflammatory response / innate immune response / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / plasma membrane Similarity search - Function | |||||||||
Biological species | Macaca mulatta (Rhesus monkey) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Zhang, Z. / Ohto, U. / Shimizu, T. | |||||||||
Citation | Journal: Immunity / Year: 2016 Title: Structural Analysis Reveals that Toll-like Receptor 7 Is a Dual Receptor for Guanosine and Single-Stranded RNA Authors: Zhang, Z. / Ohto, U. / Shibata, T. / Krayukhina, E. / Taoka, M. / Yamauchi, Y. / Tanji, H. / Isobe, T. / 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 | 5gmh.cif.gz | 346 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gmh.ent.gz | 277.6 KB | Display | PDB format |
PDBx/mmJSON format | 5gmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/5gmh ftp://data.pdbj.org/pub/pdb/validation_reports/gm/5gmh | HTTPS FTP |
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-Related structure data
Related structure data | 5gmfSC 5gmgC S: Starting model for refinement 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: 0 / 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: 0 / Auth seq-ID: 27 - 835 / Label seq-ID: 5 - 813
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 94014.656 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 (fruit flies) / References: UniProt: B3Y653 |
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-Sugars , 2 types, 15 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 683 molecules
#3: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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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: 2.79 Å3/Da / Density % sol: 55.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium sulfate, sodium citrate pH 5.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50.01 Å / Num. obs: 100054 / % possible obs: 98.8 % / Redundancy: 13.5 % / Rsym value: 0.103 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.937 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GMF Resolution: 2.2→50.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.815 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.187 / 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: 42.593 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→50.01 Å
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