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- PDB-8sj2: Structure of ternary complex of cGAS with dsDNA and bound ATP and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8sj2 | ||||||
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Title | Structure of ternary complex of cGAS with dsDNA and bound ATP and 2'-dGTP | ||||||
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![]() | TRANSFERASE/DNA / IMMUNE SYSTEM / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() regulation of type I interferon production / cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / negative regulation of DNA repair / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway ...regulation of type I interferon production / cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / negative regulation of DNA repair / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway / cGMP-mediated signaling / cellular response to exogenous dsRNA / regulation of immune response / positive regulation of type I interferon production / nucleosome binding / negative regulation of double-strand break repair via homologous recombination / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / cAMP-mediated signaling / molecular condensate scaffold activity / determination of adult lifespan / positive regulation of cellular senescence / double-stranded DNA binding / site of double-strand break / defense response to virus / nuclear body / DNA repair / innate immune response / chromatin binding / DNA damage response / GTP binding / protein homodimerization activity / DNA binding / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, S. / Sohn, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS. Authors: Wu, S. / Gabelli, S.B. / Sohn, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 387.5 KB | Display | ![]() |
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PDB format | ![]() | 311.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8eaeC ![]() 8g10C ![]() 8g1jC ![]() 8g23C ![]() 8gimC ![]() 8ginC ![]() 8gioC ![]() 8gipC ![]() 8girC ![]() 8gisC ![]() 8gitC ![]() 8shkC ![]() 8shuC ![]() 8shyC ![]() 8shzC ![]() 8si0C ![]() 8sj0C ![]() 8sj1C ![]() 8sj8C ![]() 8sktC ![]() 4lezS S: Starting model for refinement C: citing same article ( |
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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
-Protein / DNA chain , 2 types, 6 molecules ACEFIJ
#1: Protein | Mass: 42640.254 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 147-507) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Details (production host): His*6-MBP-Tev-AgeI-mcGAS CAT, Kanamycin resistance Production host: ![]() ![]() #2: DNA chain | Mass: 5514.603 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 123 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/DGT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DGT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.42 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M ammonium acetate, 32% MPD, 0.1 M Bis-Tris, pH 6.5 PH range: 6.0-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: nitrogen gas stream / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 9, 2021 |
Radiation | Monochromator: double crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→29.72 Å / Num. obs: 54457 / % possible obs: 99.3 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Χ2: 1.01 / Net I/σ(I): 12.3 / Num. measured all: 366658 |
Reflection shell | Resolution: 2.23→2.3 Å / % possible obs: 92.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.702 / Num. measured all: 24921 / Num. unique obs: 4142 / CC1/2: 0.816 / Rpim(I) all: 0.306 / Rrim(I) all: 0.768 / Χ2: 0.97 / Net I/σ(I) obs: 2.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4LEZ Resolution: 2.23→29.72 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→29.72 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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