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

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Basic information

Entry
Database: PDB / ID: 8gis
TitleStructure of Ternary Complex of mouse cGAS with dsDNA and Bound ATP: with 10mM Mg2+ and 0.5mM Mn2+
Components
  • Cyclic GMP-AMP synthase
  • Palindromic DNA18
KeywordsIMMUNE SYSTEM / TRANSFERASE/DNA / Transferase-DNA complex / cGAS / ATP and divalent metal ion
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 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 / regulation of immune response / 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
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: 2.46 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: To Be Published
Title: Structure of Ternary Complex of mouse cGAS with dsDNA and Bound ATP: with 10mM Mg2+ and 0.5mM Mn2+
Authors: Wu, S. / Sohn, J.
History
DepositionMar 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 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
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)108,70414
Polymers107,3396
Non-polymers1,3658
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.056, 98.218, 142.465
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
Details: Mouse Cyclic GMP-AMP synthase catalytic domain 147-507; three extra residues at the N terminus (G from TEV site, TG from AgeI site). Flexible residues in the coordinate were deleted.
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: custom synthesized by IDT / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 43 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.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
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: 2.46→29.54 Å / Num. obs: 40447 / % possible obs: 99.4 % / Redundancy: 5.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.044 / Rrim(I) all: 0.107 / Χ2: 1.03 / Net I/σ(I): 10.3 / Num. measured all: 225388
Reflection shellResolution: 2.46→2.56 Å / % possible obs: 95.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.546 / Num. measured all: 19823 / Num. unique obs: 4301 / CC1/2: 0.82 / Rpim(I) all: 0.28 / Rrim(I) all: 0.616 / Χ2: 0.91 / Net I/σ(I) obs: 2.6

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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: 2.46→29.54 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 3830 5.12 %
Rwork0.1919 --
obs0.1938 40447 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5830 1464 68 35 7397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.073
X-RAY DIFFRACTIONf_dihedral_angle_d23.4971470
X-RAY DIFFRACTIONf_chiral_restr0.0541151
X-RAY DIFFRACTIONf_plane_restr0.0121084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.490.35591240.29462055X-RAY DIFFRACTION78
2.49-2.520.28391340.2732668X-RAY DIFFRACTION97
2.52-2.560.32541400.28482588X-RAY DIFFRACTION96
2.56-2.590.34651380.26842558X-RAY DIFFRACTION94
2.59-2.630.32991130.27522652X-RAY DIFFRACTION97
2.63-2.670.33151390.27812660X-RAY DIFFRACTION97
2.67-2.720.27811500.25922587X-RAY DIFFRACTION97
2.72-2.760.28751210.26382617X-RAY DIFFRACTION97
2.76-2.810.33311410.26662624X-RAY DIFFRACTION97
2.81-2.870.3141530.26382633X-RAY DIFFRACTION97
2.87-2.920.28931410.26212660X-RAY DIFFRACTION97
2.92-2.990.28041330.25612630X-RAY DIFFRACTION97
2.99-3.060.28041360.24412673X-RAY DIFFRACTION97
3.06-3.130.27091460.23042608X-RAY DIFFRACTION98
3.13-3.220.26951320.22772677X-RAY DIFFRACTION98
3.22-3.310.21791230.21122679X-RAY DIFFRACTION98
3.31-3.420.28231830.21282588X-RAY DIFFRACTION97
3.42-3.540.21321550.18612681X-RAY DIFFRACTION99
3.54-3.680.26761640.1962675X-RAY DIFFRACTION99
3.68-3.850.22751640.1852667X-RAY DIFFRACTION99
3.85-4.050.2361580.17452688X-RAY DIFFRACTION100
4.05-4.310.17021240.15792740X-RAY DIFFRACTION99
4.31-4.640.16881450.14622680X-RAY DIFFRACTION100
4.64-5.10.18221500.15062685X-RAY DIFFRACTION100
5.1-5.830.19091470.15692660X-RAY DIFFRACTION99
5.84-7.330.23021110.18012736X-RAY DIFFRACTION99
7.33-29.540.16061650.12432666X-RAY DIFFRACTION99
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)
11.71240.3838-0.35282.3224-0.24441.09810.00980.0430.1269-0.0856-0.003-0.2122-0.08770.1063-0.02080.2522-0.0209-0.00470.28310.01190.27834.15426.974-20.26
22.09151.4990.23033.23770.25861.1828-0.23260.2912-0.0393-0.27390.20470.30810.0403-0.09510.02580.2947-0.06480.03720.3377-0.04540.29265.186-8.008-18.947
32.38390.63280.51731.2629-1.1282.44340.30030.6906-0.1335-0.56340.0807-0.0603-0.2279-0.3853-0.29210.59440.20430.06160.614-0.02640.505710.09623.248-31.663
41.3260.74360.5621.9514-0.23241.52270.29520.5847-0.03-0.3815-0.1031-0.15050.2114-0.5563-0.17560.59030.10390.00660.71670.01470.43839.44323.856-32.519
52.7271.1256-1.16972.88220.4531.35140.0343-0.214-0.5537-0.03160.058-0.26950.2280.5539-0.10940.48870.09120.04550.5419-0.00860.620230.734-8.576-18.151
63.1830.04550.20182.8053-0.00751.44790.0519-0.2109-0.41830.13030.17-0.3699-0.48960.4158-0.16790.5693-0.01930.11610.5959-0.16340.548130.321-6.603-18.886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 148:506 OR RESID 602:602 ) )A148 - 506
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 148:506 OR RESID 602:602 ) )A602
3X-RAY DIFFRACTION2( CHAIN C AND ( RESID 148:506 OR RESID 602:602 ) )C148 - 506
4X-RAY DIFFRACTION2( CHAIN C AND ( RESID 148:506 OR RESID 602:602 ) )C602
5X-RAY DIFFRACTION3( CHAIN E AND RESID 1:18 )E1 - 18
6X-RAY DIFFRACTION4( CHAIN F AND RESID 1:18 )F1 - 18
7X-RAY DIFFRACTION5( CHAIN I AND RESID 1:18 )I1 - 18
8X-RAY DIFFRACTION6( CHAIN J AND RESID 1:18 )J1 - 18

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