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- PDB-8sj8: Structure of binary complex of human cGAS and bound ppp(2'-5')GpG -
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Open data
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Basic information
Entry | Database: PDB / ID: 8sj8 | ||||||
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Title | Structure of binary complex of human cGAS and bound ppp(2'-5')GpG | ||||||
![]() | Cyclic GMP-AMP synthase | ||||||
![]() | TRANSFERASE / IMMUNE SYSTEM / ligands / intermediate | ||||||
Function / homology | ![]() cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway ...cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / cGMP-mediated signaling / cellular response to exogenous dsRNA / positive regulation of type I interferon production / negative regulation of double-strand break repair via homologous recombination / nucleosome binding / 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 / site of double-strand break / double-stranded DNA binding / defense response to virus / nuclear body / DNA repair / innate immune response / DNA damage response / chromatin binding / GTP binding / protein homodimerization activity / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
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 | ![]() | 153.1 KB | Display | ![]() |
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PDB format | ![]() | 117.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 792.5 KB | Display | ![]() |
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Full document | ![]() | 799.1 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8eaeC ![]() 8g10C ![]() 8g1jC ![]() 8g23C ![]() 8gimC ![]() 8ginC ![]() 8gioC ![]() 8gipC ![]() 8girC ![]() 8gisC ![]() 8gitC ![]() 8shkC ![]() 8shuC ![]() 8shyC ![]() 8shzC ![]() 8si0C ![]() 8sj0C ![]() 8sj1C ![]() 8sj2C ![]() 8sktC ![]() 4k8vS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 42974.473 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 157-522) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): His*6-MBP-Tev-AgeI-hcGAS CAT, Kanamycin resistance Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-OKR / [[( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.45 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 5mM magnesium chloride, 0.1M Tris-HCl pH8.5, and 8% (w/v) PEG8000 |
-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: Mar 9, 2022 |
Radiation | Monochromator: double crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→28.98 Å / Num. obs: 23430 / % possible obs: 98.8 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.028 / Rrim(I) all: 0.069 / Χ2: 1.02 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.171 / Num. measured all: 8463 / Num. unique obs: 1413 / CC1/2: 0.982 / Rpim(I) all: 0.075 / Rrim(I) all: 0.187 / Χ2: 0.95 / Net I/σ(I) obs: 8.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4K8V Resolution: 2.5→28.98 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.67 / 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: 2.5→28.98 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.7121 Å / Origin y: 14.5557 Å / Origin z: 17.0513 Å
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Refinement TLS group | Selection details: (chain A and resseq 161:521) or (chain A and resseq 602:602) |