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- PDB-8gin: Structure of Ternary Complex of mouse cGAS with dsDNA and Bound A... -

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Basic information

Entry
Database: PDB / ID: 8gin
TitleStructure of Ternary Complex of mouse cGAS with dsDNA and Bound ATP: with 10mM Mg2+ and 0.015mM Mn2+
Components
  • Cyclic GMP-AMP synthase
  • Palindromic DNA18
KeywordsIMMUNE SYSTEM/DNA / Transferase-DNA complex / cGAS / ATP and divalent metal / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex
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 / negative regulation of DNA repair / cGAS/STING signaling pathway / regulation of immunoglobulin production / regulation of T cell activation / pattern recognition receptor 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 / negative regulation of DNA repair / cGAS/STING signaling pathway / regulation of immunoglobulin production / regulation of T cell activation / pattern recognition receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / cGMP-mediated signaling / regulation of immune response / positive regulation of type I interferon production / negative regulation of double-strand break repair via homologous recombination / nucleosome binding / 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 / 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
ADENOSINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWu, S. / Sohn, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2024
Title: The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS.
Authors: Wu, S. / Gabelli, S.B. / Sohn, J.
History
DepositionMar 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
C: Cyclic GMP-AMP synthase
E: Palindromic DNA18
F: Palindromic DNA18
I: Palindromic DNA18
J: Palindromic DNA18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,64314
Polymers107,3396
Non-polymers1,3048
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.392, 98.709, 142.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 6 molecules ACEFIJ

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


Mass: 42640.254 Da / Num. of mol.: 2 / Fragment: catalytic domain, residues 147-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cgas, Mb21d1 / Plasmid: nHMT mCAT WT
Details (production host): His*6-MBP-Tev-AgeI-mcGAS CAT, Kanamycin resistance
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C6L5, cyclic GMP-AMP synthase
#2: DNA chain
Palindromic DNA18


Mass: 5514.603 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: ordered from IDT / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 29 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen gas stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1.891 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2022
RadiationMonochromator: horizontal bounce Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.891 Å / Relative weight: 1
ReflectionResolution: 2.75→29.78 Å / Num. obs: 28710 / % possible obs: 99 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Χ2: 1.02 / Net I/σ(I): 10.8 / Num. measured all: 186375
Reflection shellResolution: 2.75→2.9 Å / % possible obs: 94 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.552 / Num. measured all: 24848 / Num. unique obs: 3913 / CC1/2: 0.867 / Rpim(I) all: 0.233 / Rrim(I) all: 0.6 / Χ2: 1.04 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.6model building
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→29.78 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 2708 5.03 %
Rwork0.1807 --
obs0.1829 28710 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5830 1464 68 21 7383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.087
X-RAY DIFFRACTIONf_dihedral_angle_d23.881470
X-RAY DIFFRACTIONf_chiral_restr0.0541151
X-RAY DIFFRACTIONf_plane_restr0.0091084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.80.37431170.31432078X-RAY DIFFRACTION77
2.8-2.860.33491540.28532722X-RAY DIFFRACTION100
2.86-2.910.32051500.26622733X-RAY DIFFRACTION100
2.91-2.980.3031430.25872745X-RAY DIFFRACTION100
2.98-3.050.3251390.26192707X-RAY DIFFRACTION100
3.05-3.120.33161460.25072700X-RAY DIFFRACTION100
3.12-3.210.25451170.22722784X-RAY DIFFRACTION100
3.21-3.30.23791490.19762679X-RAY DIFFRACTION100
3.3-3.410.27471410.20152728X-RAY DIFFRACTION99
3.41-3.530.23281610.1892711X-RAY DIFFRACTION99
3.53-3.670.21811250.1932739X-RAY DIFFRACTION100
3.67-3.840.25521440.18732690X-RAY DIFFRACTION100
3.84-4.040.1991550.17262751X-RAY DIFFRACTION100
4.04-4.290.18921360.15472721X-RAY DIFFRACTION100
4.29-4.620.20251770.152693X-RAY DIFFRACTION100
4.62-5.080.21041390.15292736X-RAY DIFFRACTION100
5.08-5.810.22031230.16542729X-RAY DIFFRACTION100
5.82-7.310.21211480.18292733X-RAY DIFFRACTION100
7.31-29.780.14651440.12022716X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4214-0.277-0.34881.8232-0.231.28080.0035-0.0790.1931-0.01820.03710.1245-0.1269-0.0622-0.0460.332-0.0004-0.02770.3316-0.00610.36684.895826.728320.3705
21.7267-1.08060.3592.8714-0.60281.5832-0.1085-0.1742-0.0799-0.07370.0714-0.42060.11540.1520.03330.35340.04450.04830.43440.02780.428933.6039-8.336418.7272
33.2485-0.75311.11992.39881.93782.54290.2098-1.00410.040.64650.1885-0.07010.34530.2904-0.52590.5345-0.14270.0540.8067-0.01230.522128.772222.857631.6025
42.3482-0.75950.71573.5518-0.01212.08570.3393-0.8346-0.19040.646-0.03450.12980.47150.8489-0.34520.8035-0.0717-0.06940.8544-0.02810.493429.516323.42732.5288
53.488-0.8911-1.26782.5891-0.18732.1570.29070.0127-0.4424-0.27640.24830.1720.4568-0.4479-0.47010.6435-0.0677-0.03550.5410.10210.56298.0897-8.668617.7321
63.6118-0.26010.76713.480.04442.14070.20430.2107-0.2844-0.250.26360.233-0.2862-0.588-0.45210.6082-0.03230.08110.63210.14310.51268.4466-6.649218.6173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 148:506) or (chain A and resseq 602:602)
2X-RAY DIFFRACTION2(chain C and resseq 148:506) or (chain C and resseq 602:602)
3X-RAY DIFFRACTION3(chain E and resseq 1:18)
4X-RAY DIFFRACTION4(chain F and resseq 1:18)
5X-RAY DIFFRACTION5(chain I and resseq 1:18)
6X-RAY DIFFRACTION6(chain J and resseq 1:18)

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