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- PDB-9j2z: mouse cGAS catalytic domain bound with RU.521 -

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Basic information

Entry
Database: PDB / ID: 9j2z
Titlemouse cGAS catalytic domain bound with RU.521
ComponentsCyclic GMP-AMP synthase
KeywordsIMMUNE SYSTEM / cGAS / inhibitor
Function / homology
Function and homology information


regulation of type I interferon production / 2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / 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 / cGMP-mediated signaling ...regulation of type I interferon production / 2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / 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 / cGMP-mediated signaling / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / positive regulation of type I interferon production / regulation of immune response / negative regulation of double-strand break repair via homologous recombination / cAMP-mediated signaling / nucleosome binding / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / 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 / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Mab-21-like, nucleotidyltransferase domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21
Similarity search - Domain/homology
: / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsZhao, W.F. / Li, M.J. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of novel cGAS inhibitors
Authors: Zhao, W.F. / Xu, Y.C.
History
DepositionAug 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: 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
C: Cyclic GMP-AMP synthase
D: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,56211
Polymers170,0484
Non-polymers1,5137
Water00
1
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5782
Polymers42,5121
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10 Å2
ΔGint-1 kcal/mol
Surface area18470 Å2
MethodPISA
2
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9953
Polymers42,5121
Non-polymers4832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17360 Å2
MethodPISA
3
C: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9953
Polymers42,5121
Non-polymers4832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17700 Å2
MethodPISA
4
D: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9953
Polymers42,5121
Non-polymers4832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.749, 84.384, 124.676
Angle α, β, γ (deg.)90.00, 92.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42512.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cgas, Mb21d1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C6L5, cyclic GMP-AMP synthase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1EAM / (4~{S},5~{R})-2-[4,5-bis(chloranyl)-1~{H}-benzimidazol-2-yl]-5-methyl-4-[(1~{S})-3-oxidanylidene-1~{H}-2-benzofuran-1-yl]pyrazolidin-3-one


Mass: 417.245 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H14Cl2N4O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M HEPES, 0.1 M MgAc2, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 69722 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.084 / Rrim(I) all: 0.2 / Χ2: 0.801 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allΧ2% possible allRrim(I) all
2.4-2.495.61.54569030.6620.8930.6910.45499.9
2.49-2.595.61.22669300.760.9290.5510.47999.9
2.59-2.75.50.95869600.7690.9330.4350.53499.7
2.7-2.855.20.70969190.8320.9530.3350.60899.50.786
2.85-3.025.80.50269540.9270.9810.220.71999.70.549
3.02-3.265.80.3569520.9560.9890.1550.95599.80.384
3.26-3.585.50.24469700.9650.9910.1131.06899.90.269
3.58-4.15.60.18169900.9770.9940.0831.05699.80.2
4.1-5.175.50.13370040.9850.9960.0621.06199.60.148
5.17-505.30.10371400.9920.9980.051.06299.60.115

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→44.06 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 3329 4.81 %
Rwork0.2224 --
obs0.2243 69277 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11229 0 88 0 11317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02111565
X-RAY DIFFRACTIONf_angle_d1.0515621
X-RAY DIFFRACTIONf_dihedral_angle_d17.5454273
X-RAY DIFFRACTIONf_chiral_restr0.0861715
X-RAY DIFFRACTIONf_plane_restr0.0111991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.430.3089670.2941542X-RAY DIFFRACTION54
2.43-2.460.30971200.29782766X-RAY DIFFRACTION98
2.46-2.50.35921330.28622751X-RAY DIFFRACTION98
2.5-2.540.35011510.28032757X-RAY DIFFRACTION99
2.54-2.590.29941250.27152775X-RAY DIFFRACTION98
2.59-2.630.34171570.27382791X-RAY DIFFRACTION99
2.63-2.680.34671430.28852734X-RAY DIFFRACTION99
2.68-2.740.33341420.2862747X-RAY DIFFRACTION99
2.74-2.80.31031590.27262810X-RAY DIFFRACTION99
2.8-2.860.34631570.25892717X-RAY DIFFRACTION99
2.86-2.930.32771210.2572794X-RAY DIFFRACTION99
2.93-3.010.29551450.24872826X-RAY DIFFRACTION99
3.01-3.10.30741210.25482837X-RAY DIFFRACTION100
3.1-3.20.32851480.27032781X-RAY DIFFRACTION100
3.2-3.320.34231140.2692814X-RAY DIFFRACTION100
3.32-3.450.33091280.24422850X-RAY DIFFRACTION100
3.45-3.610.33881410.23782804X-RAY DIFFRACTION100
3.61-3.80.27771580.21822809X-RAY DIFFRACTION100
3.8-4.030.27291350.21042843X-RAY DIFFRACTION100
4.04-4.350.21591740.1922777X-RAY DIFFRACTION100
4.35-4.780.20241590.18172816X-RAY DIFFRACTION99
4.78-5.470.21741420.19362841X-RAY DIFFRACTION100
5.47-6.890.24361350.22792857X-RAY DIFFRACTION100
6.89-44.060.19081540.17962909X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.895 Å / Origin y: 32.5224 Å / Origin z: 35.8508 Å
111213212223313233
T0.4871 Å20.0115 Å2-0.0039 Å2-0.472 Å20.0412 Å2--0.4718 Å2
L0.1151 °2-0.0137 °2-0.1365 °2-0.1092 °20.1472 °2--0.1509 °2
S0.0193 Å °0.0741 Å °0.0616 Å °-0.0789 Å °0.004 Å °-0.0211 Å °-0.0859 Å °-0.0276 Å °-0.0163 Å °
Refinement TLS groupSelection details: all

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