+Open data
-Basic information
Entry | Database: PDB / ID: 6edb | ||||||
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Title | Crystal structure of SRY.hcGAS-21bp dsDNA complex | ||||||
Components |
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Keywords | Transferase/DNA / SRY human cGAS DNA complex / Transferase-DNA complex | ||||||
Function / homology | Function and homology information positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / male sex determination / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / cGAS/STING signaling pathway ...positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / male sex determination / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / cGAS/STING signaling pathway / regulation of immunoglobulin production / regulation of T cell activation / pattern recognition receptor signaling pathway / negative regulation of double-strand break repair via homologous recombination / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / cGMP-mediated signaling / cAMP-mediated signaling / nucleosome binding / positive regulation of type I interferon production / anatomical structure morphogenesis / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / molecular condensate scaffold activity / Deactivation of the beta-catenin transactivating complex / determination of adult lifespan / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / DNA-binding transcription factor binding / cell differentiation / nuclear body / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / innate immune response / DNA damage response / chromatin binding / chromatin / GTP binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.209 Å | ||||||
Authors | Xie, W. / Lama, L. / Adura, C. / Glickman, J.F. / Tuschl, T. / Patel, D.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Human cGAS catalytic domain has an additional DNA-binding interface that enhances enzymatic activity and liquid-phase condensation. Authors: Xie, W. / Lama, L. / Adura, C. / Tomita, D. / Glickman, J.F. / Tuschl, T. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6edb.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6edb.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 6edb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/6edb ftp://data.pdbj.org/pub/pdb/validation_reports/ed/6edb | HTTPS FTP |
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-Related structure data
Related structure data | 6edcC 6o47C 4k96S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53716.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SRY, TDF, CGAS, C6orf150, MB21D1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q05066, UniProt: Q8N884, cyclic GMP-AMP synthase #2: DNA chain | | Mass: 6745.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: DNA chain | | Mass: 6758.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Chemical | ChemComp-ZN / | |
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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: 1.72 Å3/Da / Density % sol: 28.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M L-proline, 0.1 M HEPES, pH 7.5, 8% PEG3350 (v/v), 10 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30.008 Å / Num. obs: 12639 / % possible obs: 60.4 % / Redundancy: 5.4 % / CC1/2: 0.98 / Rpim(I) all: 0.051 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 3.2→3.32 Å / Num. unique obs: 833 / CC1/2: 0.722 / Rpim(I) all: 0.338 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K96 Resolution: 3.209→30.008 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.209→30.008 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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