- PDB-7ful: Crystal Structure of human cyclic GMP-AMP synthase in complex wit... -
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Basic information
Entry
Database: PDB / ID: 7ful
Title
Crystal Structure of human cyclic GMP-AMP synthase in complex with 6-(2-chloro-4-methylphenyl)-3-[3-(methanesulfonamido)propyl]benzimidazole-4-carboxylic acid
Components
Cyclic GMP-AMP synthase
Keywords
TRANSFERASE / IMMUNE RESPONSE / NTASE / DNA SENSOR
Function / homology
Function and homology information
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 / 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 / molecular condensate scaffold activity / determination of adult lifespan / positive regulation of cellular senescence / double-stranded DNA binding / site of double-strand break / defense response to virus / nuclear body / DNA repair / innate immune response / chromatin binding / DNA damage response / GTP binding / protein homodimerization activity / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
Y
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of ...Details: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals.
Method to determine structure: MOLECULAR REPLACEMENT Starting model: inhouse model Resolution: 2.296→62.913 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.46 / Stereochemistry target values: ML Details: propy linker not well defined by electron density. sulfonamide rotated to satisfy torsion angle
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2732
664
4.82 %
RANDOM
Rwork
0.1905
13103
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obs
0.1946
13767
82.18 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
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