+Open data
-Basic information
Entry | Database: PDB / ID: 8shy | ||||||
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Title | Structure of binary complex of mouse cGAS QN and bound ATP | ||||||
Components | Cyclic GMP-AMP synthase | ||||||
Keywords | TRANSFERASE / IMMUNE SYSTEM | ||||||
Function / homology | Function and homology information 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 / 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 / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Wu, S. / Sohn, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8shy.cif.gz | 164.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8shy.ent.gz | 127 KB | Display | PDB format |
PDBx/mmJSON format | 8shy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8shy_validation.pdf.gz | 880.6 KB | Display | wwPDB validaton report |
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Full document | 8shy_full_validation.pdf.gz | 884.2 KB | Display | |
Data in XML | 8shy_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 8shy_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/8shy ftp://data.pdbj.org/pub/pdb/validation_reports/sh/8shy | HTTPS FTP |
-Related structure data
Related structure data | 8eaeC 8g10C 8g1jC 8g23C 8gimC 8ginC 8gioC 8gipC 8girC 8gisC 8gitC 8shkC 8shuC 8shzC 8si0C 8sj0C 8sj1C 8sj2C 8sj8C 8sktC 4k8vS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42638.281 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 147-507) / Mutation: E211Q, D213N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cgas, Mb21d1 / Plasmid: nHMT mCAT WT Details (production host): His*6-MBP-Tev-AgeI-mcGAS CAT, Kanamycin resistance Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C6L5, cyclic GMP-AMP synthase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-ATP / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.46 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 20% w/v PEG8000 Temp details: 4-degree Celsius in cold room |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: nitrogen gas stream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 13, 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: 1.77→28.79 Å / Num. obs: 53469 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.052 / Rrim(I) all: 0.098 / Χ2: 1 / Net I/σ(I): 8.1 / Num. measured all: 188329 |
Reflection shell | Resolution: 1.77→1.8 Å / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.665 / Num. measured all: 10555 / Num. unique obs: 2985 / CC1/2: 0.793 / Rpim(I) all: 0.406 / Rrim(I) all: 0.781 / Χ2: 1.05 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4K8V Resolution: 1.77→27.94 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 24.88 / 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: 1.77→27.94 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: -3.8406 Å / Origin y: 0.2723 Å / Origin z: 30.3376 Å
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Refinement TLS group | Selection details: (chain C and resseq 144:507) or (chain A and resseq 2:2) |