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- PDB-8shu: Structure of mouse cGAS -

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Basic information

Entry
Database: PDB / ID: 8shu
TitleStructure of mouse cGAS
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / IMMUNE SYSTEM
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / regulation of type I interferon production / 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 / : ...2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / regulation of type I interferon production / 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 / : / 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 / 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 / metal ion binding / nucleus / 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
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)42,7062
Polymers42,6401
Non-polymers651
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.892, 61.054, 105.704
Angle α, β, γ (deg.)90.00, 94.57, 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-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.32 Å3/Da / Density % sol: 62.9 %
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-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2021
RadiationMonochromator: horizontal bounce Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.71→28.76 Å / Num. obs: 58990 / % possible obs: 97.8 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.039 / Rrim(I) all: 0.055 / Χ2: 0.9 / Net I/σ(I): 10.5
Reflection shellResolution: 1.71→1.74 Å / % possible obs: 94.5 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.437 / Num. measured all: 5780 / Num. unique obs: 3022 / CC1/2: 0.73 / Rpim(I) all: 0.437 / Rrim(I) all: 0.618 / Χ2: 0.84 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.6model building
REFMAC5.8.0403refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4K8V

4k8v


Resolution: 1.71→28.76 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.205 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21139 2989 5.1 %RANDOM
Rwork0.17722 ---
obs0.17899 56000 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.339 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0 Å20.37 Å2
2---1.29 Å2-0 Å2
3---2.38 Å2
Refinement stepCycle: 1 / Resolution: 1.71→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 1 440 3395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123056
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162975
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.6524103
X-RAY DIFFRACTIONr_angle_other_deg0.5391.5776897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.625520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03810606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3372.6691451
X-RAY DIFFRACTIONr_mcbond_other3.3352.6691451
X-RAY DIFFRACTIONr_mcangle_it4.7264.7851812
X-RAY DIFFRACTIONr_mcangle_other4.7264.7881813
X-RAY DIFFRACTIONr_scbond_it4.6323.2461605
X-RAY DIFFRACTIONr_scbond_other4.6313.2491606
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2535.6622292
X-RAY DIFFRACTIONr_long_range_B_refined9.75428.983791
X-RAY DIFFRACTIONr_long_range_B_other9.73327.723645
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.712→1.756 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 215 -
Rwork0.281 4052 -
obs--95.63 %

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