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Yorodumi- PDB-6wt7: Structure of a metazoan TIR-STING receptor from C. gigas in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wt7 | ||||||
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Title | Structure of a metazoan TIR-STING receptor from C. gigas in complex with 2',3'-cGAMP | ||||||
Components | Metazoan TIR-STING fusion | ||||||
Keywords | IMMUNE SYSTEM / TIR domain / cyclic dinucleotide receptor / immune effector | ||||||
Function / homology | Function and homology information ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NADP+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of type I interferon production / activation of innate immune response / autophagy / nucleotide binding / signal transduction Similarity search - Function | ||||||
Biological species | Crassostrea gigas (Pacific oyster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Morehouse, B.R. / Govande, A.A. / Millman, A. / Keszei, A.F.A. / Lowey, B. / Ofir, G. / Shao, S. / Sorek, R. / Kranzusch, P.J. | ||||||
Citation | Journal: Nature / Year: 2020 Title: STING cyclic dinucleotide sensing originated in bacteria. Authors: Morehouse, B.R. / Govande, A.A. / Millman, A. / Keszei, A.F.A. / Lowey, B. / Ofir, G. / Shao, S. / Sorek, R. / Kranzusch, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wt7.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wt7.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 6wt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/6wt7 ftp://data.pdbj.org/pub/pdb/validation_reports/wt/6wt7 | HTTPS FTP |
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-Related 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: 47063.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Crassostrea gigas (Pacific oyster) / Gene: XP_011430837.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DUE1*PLUS |
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#2: Chemical | ChemComp-1SY / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M ammonium citrate pH 7.0, 20% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→46.82 Å / Num. obs: 10981 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 89.21 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.034 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.9→3.08 Å / Num. unique obs: 1763 / CC1/2: 0.881 / Rpim(I) all: 0.408 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→46.82 Å / SU ML: 0.3987 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.565
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→46.82 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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