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

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Basic information

Entry
Database: PDB / ID: 8shy
TitleStructure of binary complex of mouse cGAS QN and bound ATP
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / IMMUNE SYSTEM
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 / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING 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 / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway / cGMP-mediated signaling / cellular response to exogenous dsRNA / 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 / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol
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 / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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)43,2113
Polymers42,6381
Non-polymers5732
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-1 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.112, 60.968, 104.352
Angle α, β, γ (deg.)90.00, 94.59, 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: 42638.281 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 147-507) / Mutation: E211Q, D213N
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.28 Å3/Da / Density % sol: 62.46 %
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
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-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: 1.77→28.79 Å / Num. obs: 53469 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.052 / Rrim(I) all: 0.098 / Χ2: 1 / Net I/σ(I): 8.1 / Num. measured all: 188329
Reflection shellResolution: 1.77→1.8 Å / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.665 / Num. measured all: 10555 / Num. unique obs: 2985 / CC1/2: 0.793 / Rpim(I) all: 0.406 / Rrim(I) all: 0.781 / Χ2: 1.05 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.6model building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4K8V

4k8v


Resolution: 1.77→27.94 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 1996 3.73 %
Rwork0.204 --
obs0.2044 53458 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→27.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 32 122 3108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.941
X-RAY DIFFRACTIONf_dihedral_angle_d7.765398
X-RAY DIFFRACTIONf_chiral_restr0.054445
X-RAY DIFFRACTIONf_plane_restr0.009525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.38931360.33053602X-RAY DIFFRACTION97
1.81-1.860.31851520.28573621X-RAY DIFFRACTION99
1.86-1.920.27141290.25993660X-RAY DIFFRACTION99
1.92-1.980.2761470.23733643X-RAY DIFFRACTION99
1.98-2.050.23551420.22223668X-RAY DIFFRACTION99
2.05-2.130.22241370.22123669X-RAY DIFFRACTION99
2.13-2.230.27171380.21383652X-RAY DIFFRACTION99
2.23-2.350.2141420.20513704X-RAY DIFFRACTION99
2.35-2.490.22261440.21623683X-RAY DIFFRACTION99
2.49-2.690.26221450.21983677X-RAY DIFFRACTION100
2.69-2.960.24421480.23043693X-RAY DIFFRACTION100
2.96-3.380.23431450.21593718X-RAY DIFFRACTION100
3.38-4.260.19331400.17233697X-RAY DIFFRACTION99
4.26-27.940.15171510.17313775X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -3.8406 Å / Origin y: 0.2723 Å / Origin z: 30.3376 Å
111213212223313233
T0.1656 Å2-0.008 Å2-0.0258 Å2-0.2088 Å20.0017 Å2--0.1505 Å2
L0.8516 °20.1121 °2-0.3453 °2-1.6288 °20.0148 °2--0.6647 °2
S-0.0476 Å °0.0968 Å °0.063 Å °-0.0393 Å °0.0595 Å °0.0649 Å °0.0047 Å °-0.0532 Å °0.0027 Å °
Refinement TLS groupSelection details: (chain C and resseq 144:507) or (chain A and resseq 2:2)

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