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- PDB-8g23: Structure of Ternary Complex of cGAS with dsDNA and Bound pppIpA -

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Basic information

Entry
Database: PDB / ID: 8g23
TitleStructure of Ternary Complex of cGAS with dsDNA and Bound pppIpA
Components
  • Cyclic GMP-AMP synthase
  • Palindromic DNA18
KeywordsIMMUNE SYSTEM/DNA / Transferase-DNA complex / cGAS / intermediate / 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 / Chem-VWX / 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: 2.71 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
DepositionFeb 3, 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)108,86312
Polymers107,3396
Non-polymers1,5246
Water1,06359
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)77.720, 98.893, 142.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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 / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 65 molecules

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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, 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: Chemical ChemComp-VWX / [[(2~{R},3~{R},4~{R},5~{R})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 837.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N9O20P4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 51.66 %
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: Aug 12, 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: 2.7→29.68 Å / Num. obs: 30386 / % possible obs: 99 % / Redundancy: 5.4 % / Biso Wilson estimate: 56.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.045 / Rrim(I) all: 0.106 / Χ2: 1.01 / Net I/σ(I): 10.7 / Num. measured all: 163259
Reflection shellResolution: 2.7→2.84 Å / % possible obs: 93.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.779 / Num. measured all: 20398 / Num. unique obs: 3771 / CC1/2: 0.74 / Rpim(I) all: 0.362 / Rrim(I) all: 0.861 / Χ2: 1.01 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→29.68 Å / SU ML: 0.3284 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.6278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1997 6.73 %RANDOM
Rwork0.1904 27674 --
obs0.1944 29671 97.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.64 Å2
Refinement stepCycle: LAST / Resolution: 2.71→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5703 1464 88 59 7314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097552
X-RAY DIFFRACTIONf_angle_d1.105610478
X-RAY DIFFRACTIONf_chiral_restr0.05521141
X-RAY DIFFRACTIONf_plane_restr0.01131060
X-RAY DIFFRACTIONf_dihedral_angle_d24.43121473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.770.29541270.23371761X-RAY DIFFRACTION88.64
2.77-2.850.28671410.24691949X-RAY DIFFRACTION97.57
2.85-2.930.33261400.23321939X-RAY DIFFRACTION96.92
2.93-3.030.34941400.24981940X-RAY DIFFRACTION97.01
3.03-3.130.30971430.23061979X-RAY DIFFRACTION97.56
3.14-3.260.26811410.20341958X-RAY DIFFRACTION97.36
3.26-3.410.26881440.19951977X-RAY DIFFRACTION97.79
3.41-3.590.24711420.20351998X-RAY DIFFRACTION98.75
3.59-3.810.24691440.19071996X-RAY DIFFRACTION98.75
3.81-4.110.24641450.17372001X-RAY DIFFRACTION98.49
4.11-4.520.21461460.16162026X-RAY DIFFRACTION98.82
4.52-5.170.23261450.16642008X-RAY DIFFRACTION97.46
5.17-6.50.26281460.19092021X-RAY DIFFRACTION97.17
6.5-29.680.19741530.17432121X-RAY DIFFRACTION97.3
Refinement TLS params.Method: refined / Origin x: 19.5901608079 Å / Origin y: 9.12033736847 Å / Origin z: -20.62287441 Å
111213212223313233
T0.236681692465 Å20.00584201576904 Å20.0130044692582 Å2-0.293523111455 Å2-0.00830960192435 Å2--0.183639223269 Å2
L0.937045554857 °20.493005016168 °2-0.208805354748 °2-1.54104915025 °20.0466605604901 °2--0.448840860809 °2
S-0.0325687332779 Å °0.150205929379 Å °-0.00305712407667 Å °-0.0447026785373 Å °0.00825371240944 Å °-0.0131216254086 Å °0.0177796624546 Å °-0.0692333824223 Å °8.13480991499E-5 Å °
Refinement TLS groupSelection details: all

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