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- PDB-8shk: Structure of binary complex of mouse cGAS and bound ATP -

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Basic information

Entry
Database: PDB / ID: 8shk
TitleStructure of binary complex of mouse cGAS and bound ATP
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / IMMUNE SYSTEM
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 / negative regulation of DNA repair / regulation of immunoglobulin production / 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 / negative regulation of DNA repair / regulation of immunoglobulin production / 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 / nucleosome binding / positive regulation of defense response to virus by host / activation of innate immune response / phosphatidylinositol-4,5-bisphosphate binding / cAMP-mediated signaling / 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
ADENOSINE-5'-TRIPHOSPHATE / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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
DepositionApr 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 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

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Assembly

Deposited unit
C: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2133
Polymers42,6401
Non-polymers5732
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-1 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.112, 61.231, 105.727
Angle α, β, γ (deg.)90.00, 94.36, 90.00
Int Tables number5
Space group name H-MI121

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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: 42640.254 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP 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: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
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: 3.33 Å3/Da / Density % sol: 63.11 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 20% w/v PEG8000
PH range: 6.0-7.0 / Temp details: 4-degree Celsius in cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 13, 2021
RadiationMonochromator: double crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.71→28.79 Å / Num. obs: 60461 / % possible obs: 99.1 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.042 / Rrim(I) all: 0.08 / Χ2: 0.97 / Net I/σ(I): 10.6 / Num. measured all: 210242
Reflection shellResolution: 1.71→1.74 Å / % possible obs: 96 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.817 / Num. measured all: 10278 / Num. unique obs: 3113 / CC1/2: 0.637 / Rpim(I) all: 0.526 / Rrim(I) all: 0.974 / Χ2: 0.93 / Net I/σ(I) obs: 1.6

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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
Starting model: PDB entry 4LEZ

4lez


Resolution: 1.71→28.79 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.21 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 2966 4.91 %
Rwork0.1934 --
obs0.195 60443 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 32 322 3305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.852
X-RAY DIFFRACTIONf_dihedral_angle_d7.667397
X-RAY DIFFRACTIONf_chiral_restr0.053443
X-RAY DIFFRACTIONf_plane_restr0.009524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.740.30871370.3082638X-RAY DIFFRACTION96
1.74-1.770.31991230.29092721X-RAY DIFFRACTION98
1.77-1.80.32341350.27532711X-RAY DIFFRACTION99
1.8-1.830.27551290.24842702X-RAY DIFFRACTION99
1.83-1.870.31561390.25672731X-RAY DIFFRACTION99
1.87-1.910.26371660.24452713X-RAY DIFFRACTION99
1.91-1.960.31351450.22462695X-RAY DIFFRACTION100
1.96-20.25951640.21662728X-RAY DIFFRACTION99
2-2.060.22221410.19332720X-RAY DIFFRACTION99
2.06-2.120.21161500.19192713X-RAY DIFFRACTION99
2.12-2.190.23591360.18262750X-RAY DIFFRACTION99
2.19-2.270.23681320.18662746X-RAY DIFFRACTION100
2.27-2.360.23321440.1852759X-RAY DIFFRACTION99
2.36-2.460.22931380.18462725X-RAY DIFFRACTION100
2.46-2.590.22871360.19132777X-RAY DIFFRACTION100
2.59-2.760.20511520.1982753X-RAY DIFFRACTION100
2.76-2.970.20131470.20082740X-RAY DIFFRACTION100
2.97-3.270.24371370.19072751X-RAY DIFFRACTION99
3.27-3.740.19511540.17832761X-RAY DIFFRACTION99
3.74-4.710.18591280.16032814X-RAY DIFFRACTION99
4.71-28.790.24571330.18992829X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.1928 Å / Origin y: -30.3003 Å / Origin z: -21.8099 Å
111213212223313233
T0.1451 Å2-0.0046 Å2-0.0198 Å2-0.185 Å2-0.0031 Å2--0.1331 Å2
L0.9632 °20.2018 °2-0.4021 °2-1.7388 °2-0.0799 °2--0.6014 °2
S-0.0251 Å °0.0963 Å °0.0858 Å °-0.0602 Å °0.0373 Å °0.0212 Å °-0.0066 Å °-0.0449 Å °-0.0065 Å °
Refinement TLS groupSelection details: (chain C and resseq 144:506) or (chain A and resseq 2:2)

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