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- PDB-8g2q: Structure of Ternary Complex of mouse cGAS with dsDNA and Bound GTP -

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Basic information

Entry
Database: PDB / ID: 8g2q
TitleStructure of Ternary Complex of mouse cGAS with dsDNA and Bound GTP
Components
  • Cyclic GMP-AMP synthase
  • Palindromic DNA18
KeywordsTRANSFERASE/DNA / IMMUNE SYSTEM/DNA / TRANSFERASE-DNA complex
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 / nucleus / metal ion binding / 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
GUANOSINE-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: 2.37 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 GTP
Authors: Wu, S. / Sohn, J.
History
DepositionFeb 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 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)109,60914
Polymers107,3376
Non-polymers2,2728
Water2,666148
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)78.294, 98.675, 142.827
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: 42639.266 Da / Num. of mol.: 2 / Mutation: D307N
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 / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 156 molecules

#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.57 Å3/Da / Density % sol: 52.14 % / Description: polarizes nicely.
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: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2022
RadiationMonochromator: horizontal bounce Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.37→29.66 Å / Num. obs: 45595 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Χ2: 1.03 / Net I/σ(I): 11.8 / Num. measured all: 305132
Reflection shellResolution: 2.37→2.45 Å / % possible obs: 95.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.804 / Num. measured all: 28408 / Num. unique obs: 4211 / CC1/2: 0.781 / Rpim(I) all: 0.328 / Rrim(I) all: 0.87 / Χ2: 1.08 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.6model building
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→28.93 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 1999 4.4 %
Rwork0.2015 --
obs0.2034 45456 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5853 1464 132 148 7597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097753
X-RAY DIFFRACTIONf_angle_d1.08610761
X-RAY DIFFRACTIONf_dihedral_angle_d27.8541524
X-RAY DIFFRACTIONf_chiral_restr0.0541163
X-RAY DIFFRACTIONf_plane_restr0.0121091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.430.31011340.26492914X-RAY DIFFRACTION95
2.43-2.490.29591420.24593065X-RAY DIFFRACTION100
2.49-2.570.28731410.24413066X-RAY DIFFRACTION100
2.57-2.650.30761410.25853079X-RAY DIFFRACTION100
2.65-2.750.31791420.24653093X-RAY DIFFRACTION100
2.75-2.860.32481420.2453088X-RAY DIFFRACTION100
2.86-2.990.29051430.24073094X-RAY DIFFRACTION100
2.99-3.140.2881410.24783086X-RAY DIFFRACTION100
3.14-3.340.24051430.21453099X-RAY DIFFRACTION100
3.34-3.60.24081440.19433127X-RAY DIFFRACTION100
3.6-3.960.24241440.19143128X-RAY DIFFRACTION100
3.96-4.530.21331450.17333141X-RAY DIFFRACTION100
4.53-5.70.20961450.1773171X-RAY DIFFRACTION100
5.7-28.930.21221520.17573306X-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)
12.52061.21690.54924.16720.37121.9728-0.0188-0.0179-0.0169-0.1502-0.06660.43420.0589-0.13120.03080.2311-0.00790.04920.2835-0.06780.29494.902-27.114-20.282
22.92671.5152-0.154.7714-0.45271.8253-0.25430.21550.2167-0.37860.1391-0.2931-0.1190.14150.08940.3214-0.0685-0.04570.33180.06340.278734.0267.842-19.213
32.76191.1522-1.15881.89921.49193.6170.21891.05330.0752-0.9199-0.04540.1170.327-0.0009-0.15720.7390.2522-0.03580.84260.07130.54129.08-23.411-31.796
42.1270.4067-1.17112.78710.32271.6730.41830.89480.0469-0.4513-0.3416-0.0251-0.46980.8123-0.02840.71410.08950.01870.90490.01680.504729.721-24.042-32.589
53.69131.16091.48053.1397-1.39081.66450.0613-0.26810.8222-0.11730.17590.4321-0.2858-0.8461-0.31480.52030.1751-0.05040.509-0.04170.75958.3358.78-18.351
65.06770.1621-0.01953.6026-1.16240.9739-0.0574-0.71990.51670.00990.16440.80220.0931-0.4891-0.04040.64460.0165-0.15410.70560.07590.67238.7586.804-19.018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 148:507 OR RESID 604:604 ) )A148 - 507
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 148:507 OR RESID 604:604 ) )A604
3X-RAY DIFFRACTION2( CHAIN C AND ( RESID 149:507 OR RESID 604:604 ) )C149 - 507
4X-RAY DIFFRACTION2( CHAIN C AND ( RESID 149:507 OR RESID 604:604 ) )C604
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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