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- PDB-7zvk: Crystal structure of human STING in complex with 3',3'-c-(2'F,2'd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zvk | ||||||||||||||||||||||||||||||
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Title | Crystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP-![]() Stimulator of interferon protein | ![]() ANTIVIRAL PROTEIN / sting / antiviral / activator | Function / homology | ![]() 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 | ![]() Method | ![]() ![]() ![]() ![]() Klima, M. / Smola, M. / Boura, E. | Funding support | 1items |
![]() ![]() Title: Crystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP- Authors: Klima, M. / Smola, M. / Boura, E. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.8 KB | Display | ![]() |
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PDB format | ![]() | 62.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ksyS 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: 23189.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-K1L / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→45.93 Å / Num. obs: 9289 / % possible obs: 99.84 % / Redundancy: 8.2 % / Biso Wilson estimate: 70.95 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.2001 / Rpim(I) all: 0.07408 / Rrim(I) all: 0.2138 / Net I/σ(I): 9.77 |
Reflection shell | Resolution: 2.83→2.931 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.739 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 898 / CC1/2: 0.488 / CC star: 0.81 / Rpim(I) all: 0.6284 / Rrim(I) all: 1.852 / % possible all: 99.78 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ksy Resolution: 2.83→45.93 Å / SU ML: 0.4121 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.7836 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: 74.31 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→45.93 Å
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Refine LS restraints |
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LS refinement shell |
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