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- PDB-8ime: Human cGAS catalytic domain bound with baicalin -

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Basic information

Entry
Database: PDB / ID: 8ime
TitleHuman cGAS catalytic domain bound with baicalin
ComponentsCyclic GMP-AMP synthase
KeywordsIMMUNE SYSTEM / cGAS / inhibitor / baicalin
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 / 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 ...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 / 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 / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / 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 / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21
Similarity search - Domain/homology
Chem-0XE / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsZhao, W.F. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Chem. / Year: 2023
Title: Discovery of novel cGAS inhibitors based on natural flavonoids.
Authors: Li, J. / Xiong, M. / Liu, J. / Zhang, F. / Li, M. / Zhao, W. / Xu, Y.
History
DepositionMar 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5426
Polymers85,5192
Non-polymers1,0244
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.872, 47.360, 87.993
Angle α, β, γ (deg.)90.00, 111.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cyclic GMP-AMP synthase / / cGAMP synthase / cGAS / h-cGAS / 2'3'-cGAMP synthase / Mab-21 domain-containing protein 1


Mass: 42759.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGAS, C6orf150, MB21D1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N884, cyclic GMP-AMP synthase
#2: Chemical ChemComp-0XE / 5,6-dihydroxy-4-oxo-2-phenyl-4H-chromen-7-yl beta-D-glucopyranosiduronic acid / Baicalin / Baicalin


Mass: 446.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18O11 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 18-20% V/V PEG 3350, 0.2 M AMMONIUM CIRTATE (pH 7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 25062 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Rrim(I) all: 0.089 / Χ2: 0.874 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.65-2.75.71.4112030.5250.830.6351.5510.87399.3
2.7-2.746.31.34912260.6450.8860.5781.470.86699.7
2.74-2.86.61.21812790.7050.9090.5071.3210.88299.6
2.8-2.856.81.01312380.770.9330.4151.0960.85299.5
2.85-2.926.70.73412010.8470.9580.3030.7950.87599.7
2.92-2.986.60.612790.9060.9750.2490.6510.91999.7
2.98-3.066.40.46512260.9160.9780.1980.5060.94899.7
3.06-3.146.30.34512210.9490.9870.1480.3760.94699.7
3.14-3.236.40.29912590.9660.9910.1270.3250.98799.8
3.23-3.346.90.24912570.9760.9940.1010.270.97499.8
3.34-3.466.90.17812350.9830.9960.0720.1920.97999.8
3.46-3.66.90.13512640.9880.9970.0550.1460.98699.8
3.6-3.766.80.10612390.9890.9970.0440.1150.971100
3.76-3.966.50.0912610.9870.9970.0390.0980.96299.9
3.96-4.216.30.0712550.9930.9980.030.0770.85799.9
4.21-4.536.80.0612450.9930.9980.0250.0660.83100
4.53-4.996.80.05612770.9950.9990.0240.0610.75499.9
4.99-5.716.60.05312710.9950.9990.0220.0580.72899.9
5.71-7.196.30.0512890.9950.9990.0210.0540.67199.8
7.19-506.10.04113370.9970.9990.0180.0450.61299.6

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-3000data scaling
HKL-30003.25data reduction
PHASER2.61phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→36.12 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 1011 4.8 %
Rwork0.2167 --
obs0.2195 21065 84.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→36.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 66 16 5008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025087
X-RAY DIFFRACTIONf_angle_d0.5196868
X-RAY DIFFRACTIONf_dihedral_angle_d4.966722
X-RAY DIFFRACTIONf_chiral_restr0.038785
X-RAY DIFFRACTIONf_plane_restr0.003858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.770.3645680.30691024X-RAY DIFFRACTION31
2.77-2.940.33021120.25942025X-RAY DIFFRACTION60
2.94-3.170.31941690.24553289X-RAY DIFFRACTION98
3.17-3.490.31221690.23133366X-RAY DIFFRACTION100
3.49-40.26451620.20373421X-RAY DIFFRACTION100
4-5.030.24861690.18843417X-RAY DIFFRACTION100
5.03-36.120.2431620.21483512X-RAY DIFFRACTION99

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