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Open data
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Basic information
Entry | Database: PDB / ID: 8si0 | ||||||
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Title | Structure of binary complex of human cGAS and bound cGAMP | ||||||
![]() | Cyclic GMP-AMP synthase | ||||||
![]() | TRANSFERASE / IMMUNE SYSTEM | ||||||
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 | ![]() | 157.6 KB | Display | ![]() |
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PDB format | ![]() | 121.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 905 KB | Display | ![]() |
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Full document | ![]() | 915.3 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 19.8 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 ![]() 8sj0C ![]() 8sj1C ![]() 8sj2C ![]() 8sj8C ![]() 8sktC ![]() 4o67S 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-1SY / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.99 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 5 mM magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 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 16M / Detector: PIXEL / Date: Feb 4, 2022 |
Radiation | Monochromator: horizontal bounce Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→27.85 Å / Num. obs: 10385 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.032 / Rrim(I) all: 0.072 / Χ2: 1 / Net I/σ(I): 15.3 / Num. measured all: 47898 |
Reflection shell | Resolution: 2.7→2.83 Å / % possible obs: 99.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.161 / Num. measured all: 6487 / Num. unique obs: 1374 / CC1/2: 0.984 / Rpim(I) all: 0.083 / Rrim(I) all: 0.182 / Χ2: 0.94 / Net I/σ(I) obs: 7.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4O67 Resolution: 2.7→27.85 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.57 / 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: 2.7→27.85 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: 13.4772 Å / Origin y: -14.1336 Å / Origin z: -16.7636 Å
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Refinement TLS group | Selection details: (chain A and resseq 161:521) or (chain A and resseq 602:602) |