[English] 日本語
![](img/lk-miru.gif)
- PDB-7zwl: Crystal structure of human STING in complex with 3',3'-c-di-(2'F,... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7zwl | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human STING in complex with 3',3'-c-di-(2'F,2'd![]()
![]() ANTIVIRAL PROTEIN / sting / antiviral / activator | Function / homology | ![]() SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / 2',3'-cyclic GMP-AMP binding / SUMOylation of SUMOylation proteins / cyclic-di-GMP binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / reticulophagy / ubiquitin-like protein ligase binding / autophagosome membrane / positive regulation of macroautophagy / protein sumoylation / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / condensed nuclear chromosome / PML body / protein tag activity / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm / identical protein binding / nucleus 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-di-(2'F,2'd Authors: Klima, M. / Smola, M. / Boura, E. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 116.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 80.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 908.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 913.9 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 26.1 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 on special symmetry positions |
|
-
Components
#1: Protein | Mass: 23189.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 11204.536 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15 / Production host: ![]() ![]() #3: Chemical | ChemComp-K43 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.31 % |
---|---|
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 6M / Detector: PIXEL / Date: Jan 24, 2019 |
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→15.96 Å / Num. obs: 35943 / % possible obs: 99.69 % / Redundancy: 22.7 % / Biso Wilson estimate: 33.8 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.2265 / Rpim(I) all: 0.04809 / Rrim(I) all: 0.2316 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2→2.071 Å / Redundancy: 22.9 % / Rmerge(I) obs: 3.083 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 3515 / CC1/2: 0.438 / CC star: 0.781 / Rpim(I) all: 0.653 / Rrim(I) all: 3.152 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4ksy Resolution: 2→15.96 Å / SU ML: 0.2546 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4384 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: 47.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|