[English] 日本語
![](img/lk-miru.gif)
- PDB-8a2x: Crystal structure of human STING in complex with 3',3'-c-(2'F,2'd... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8a2x | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP(S)-2'F,2'd![]() 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(S)-2'F,2'd Authors: Klima, M. / Smola, M. / Boura, E. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 53.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 34.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 888.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 888.2 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ksyS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 23189.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-KZA / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.02 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 23, 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: 3→39.25 Å / Num. obs: 4778 / % possible obs: 99.21 % / Redundancy: 11.6 % / Biso Wilson estimate: 62.71 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.2494 / Rpim(I) all: 0.07549 / Rrim(I) all: 0.261 / Net I/σ(I): 9.86 |
Reflection shell | Resolution: 3→3.108 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.493 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 443 / CC1/2: 0.69 / CC star: 0.904 / Rpim(I) all: 0.4293 / Rrim(I) all: 1.555 / % possible all: 98.23 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4ksy Resolution: 3→39.25 Å / SU ML: 0.3518 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7232 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.72 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→39.25 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell |
|