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Yorodumi- PDB-8ecc: Structure of Ternary Complex of cGAS with dsDNA and Bound 5-pppI(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ecc | ||||||
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Title | Structure of Ternary Complex of cGAS with dsDNA and Bound 5-pppI(2,5)pA | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Transferase-DNA complex / cGAS / 5-pppI(2 / 5)pA / IMMUNE SYSTEM / TRANSFERASE | ||||||
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 / regulation of immunoglobulin production / negative regulation of DNA repair / 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 / regulation of immunoglobulin production / negative regulation of DNA repair / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway / cGMP-mediated signaling / cellular response to exogenous dsRNA / positive regulation of type I interferon production / regulation of immune response / 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 / determination of adult lifespan / molecular condensate scaffold activity / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / nuclear body / innate immune response / DNA repair / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Wu, S. / Sohn, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of Ternary Complex of cGAS with dsDNA and Bound 5-pppI(2,5)pA Authors: Wu, S. / Sohn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ecc.cif.gz | 380.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ecc.ent.gz | 304.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ecc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ecc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8ecc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8ecc_validation.xml.gz | 28 KB | Display | |
Data in CIF | 8ecc_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/8ecc ftp://data.pdbj.org/pub/pdb/validation_reports/ec/8ecc | HTTPS FTP |
-Related structure data
Related structure data | 7uuxS S: Starting model for refinement |
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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
-Protein / DNA chain , 2 types, 6 molecules ACEFIJ
#1: Protein | Mass: 42640.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Mouse Cyclic GMP-AMP synthase catalytic domain 147-507; There are three extra residues GTG at the N terminus (G from TEV site, TG from AgeI site). Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C6L5, cyclic GMP-AMP synthase #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, 66 molecules
#3: Chemical | ChemComp-ATP / | ||||||
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#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-VWX / [[( | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.91 % |
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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, with 0.1 M Bis-Tris pH 6.5 PH range: 6.0-7.0 / 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-2 / Wavelength: 0.979307 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 12, 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: 0.979307 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.44→80.9 Å / Num. obs: 34204 / % possible obs: 83.2 % / Redundancy: 1.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.067 / Rrim(I) all: 0.095 / Net I/σ(I): 8.9 / Num. measured all: 64682 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7UUX Resolution: 2.44→80.9 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.914 / SU B: 28.597 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.887 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.19 Å2 / Biso mean: 56.093 Å2 / Biso min: 23.44 Å2
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Refinement step | Cycle: final / Resolution: 2.44→80.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.44→2.501 Å / Rfactor Rfree error: 0
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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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