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- PDB-8a2i: human STING in complex with 2'-3'-cyclic-GMP-7-deaza(4-(2-naphthy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8a2i | ||||||
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Title | human STING in complex with 2'-3'-cyclic-GMP-7-deaza(4-(2-naphthyl)phenyl)-AMP | ||||||
![]() | Stimulator of interferon genes protein | ||||||
![]() | IMMUNE SYSTEM / Complex / STING / cyclic dinucleotide | ||||||
Function / homology | ![]() STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / proton channel activity / 2',3'-cyclic GMP-AMP binding / STING mediated induction of host immune responses / cyclic-di-GMP binding / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway ...STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / proton channel activity / 2',3'-cyclic GMP-AMP binding / STING mediated induction of host immune responses / cyclic-di-GMP binding / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / reticulophagy / pattern recognition receptor signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / autophagosome membrane / antiviral innate immune response / positive regulation of macroautophagy / cellular response to organic cyclic compound / autophagosome assembly / autophagosome / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / activation of innate immune response / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / cytoplasmic vesicle membrane / positive regulation of DNA-binding transcription factor activity / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / protein complex oligomerization / regulation of inflammatory response / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / endosome / Golgi membrane / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vavrina, Z. / Brynda, J. / Rezacova, P. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Design, Synthesis, and Biochemical and Biological Evaluation of Novel 7-Deazapurine Cyclic Dinucleotide Analogues as STING Receptor Agonists. Authors: Vavrina, Z. / Perlikova, P. / Milisavljevic, N. / Chevrier, F. / Smola, M. / Smith, J. / Dejmek, M. / Havlicek, V. / Budesinsky, M. / Liboska, R. / Vanekova, L. / Brynda, J. / Boura, E. / ...Authors: Vavrina, Z. / Perlikova, P. / Milisavljevic, N. / Chevrier, F. / Smola, M. / Smith, J. / Dejmek, M. / Havlicek, V. / Budesinsky, M. / Liboska, R. / Vanekova, L. / Brynda, J. / Boura, E. / Rezacova, P. / Hocek, M. / Birkus, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.1 KB | Display | ![]() |
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PDB format | ![]() | 67.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 940.9 KB | Display | ![]() |
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Full document | ![]() | 944.9 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a2hC ![]() 8a2jC ![]() 8a2kC ![]() 4ksyS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27097.514 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-KWF / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 100 mM PIPES [pH 7.0], 100 mM magnesium formate dihydrate, 100 mM rubidium chloride, 25% (w/v) PEG smear high |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.12→47.1 Å / Num. obs: 22258 / % possible obs: 95 % / Redundancy: 6.405 % / Biso Wilson estimate: 41.497 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.164 / Χ2: 0.775 / Net I/σ(I): 8.76 / Num. measured all: 142559 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KSY Resolution: 2.16→47.1 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.936 / SU B: 0.007 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 91.32 Å2 / Biso mean: 41.895 Å2 / Biso min: 19.3 Å2
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Refinement step | Cycle: final / Resolution: 2.16→47.1 Å
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LS refinement shell | Resolution: 2.16→2.214 Å / Rfactor Rfree error: 0
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