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Yorodumi- PDB-7zv0: Crystal structure of human STING in complex with 3',3'-c-(2'F,2'd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zv0 | ||||||||||||||||||||||||||||||
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Title | Crystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP-2'F,2'dComponents | Stimulator of interferon protein | Keywords | ANTIVIRAL PROTEIN / sting / antiviral / activator | Function / homology | Function and homology information 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle ...2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm Similarity search - Function Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | Authors | Klima, M. / Smola, M. / Boura, E. | Funding support | 1items |
Citation | Journal: To Be Published | Title: Crystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP-2'F,2'd Authors: Klima, M. / Smola, M. / Boura, E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zv0.cif.gz | 54 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zv0.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zv0_validation.pdf.gz | 901.8 KB | Display | wwPDB validaton report |
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Full document | 7zv0_full_validation.pdf.gz | 901.8 KB | Display | |
Data in XML | 7zv0_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 7zv0_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/7zv0 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/7zv0 | HTTPS FTP |
-Related structure data
Related structure data | 4ksyS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23189.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STING, LOC340061, hCG_1782396 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R3XZB7 |
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#2: Chemical | ChemComp-K1C / |
#3: Water | ChemComp-HOH / |
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: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Lithium acetate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→34.08 Å / Num. obs: 10263 / % possible obs: 99.56 % / Redundancy: 9.5 % / Biso Wilson estimate: 29.16 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1526 / Rpim(I) all: 0.05162 / Rrim(I) all: 0.1614 / Net I/σ(I): 14.08 |
Reflection shell | Resolution: 2.31→2.393 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 983 / CC1/2: 0.801 / CC star: 0.943 / Rpim(I) all: 0.3036 / Rrim(I) all: 0.8729 / % possible all: 97.04 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ksy Resolution: 2.31→34.08 Å / SU ML: 0.2559 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6663 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→34.08 Å
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Refine LS restraints |
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LS refinement shell |
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