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- PDB-7uyq: Structure of GTP binds to Cyclic GMP AMP synthase (cGAS) through ... -

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Basic information

Entry
Database: PDB / ID: 7uyq
TitleStructure of GTP binds to Cyclic GMP AMP synthase (cGAS) through Mg coordination
Components
  • Cyclic GMP-AMP synthase
  • Palindromic DNA18
KeywordsTransferase/DNA / GTP / Transferase-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 double-strand break repair via homologous recombination / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / cGMP-mediated signaling / cAMP-mediated signaling / nucleosome binding / positive regulation of type I interferon production / regulation of immune response / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / 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
GUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsWu, S. / Gabelli, S.B. / 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 GTP binds to Cyclic GMP AMP synthase (cGAS) through Mg coordination
Authors: Wu, S. / Gabelli, S.B. / Sohn, J.S.
History
DepositionMay 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)109,60714
Polymers107,3356
Non-polymers2,2728
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Interaction was confirmed by ITC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-69 kcal/mol
Surface area41410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.745, 99.578, 142.001
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 42638.281 Da / Num. of mol.: 2 / Mutation: E211Q, D213N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cgas, Mb21d1 / Plasmid: nHMT mCAT QN
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: isolated from a natural source / Source: (natural) DNA molecule (others) / Plasmid details: ordered from IDT

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Non-polymers , 4 types, 55 molecules

#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine 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 / Feature type: SUBJECT OF INVESTIGATION
#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 / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
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: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 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: 2.57→28.92 Å / Num. obs: 35696 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.57-2.686.60.812728741390.760.3350.8782.495.9
8.9-28.9160.04256509460.9970.0180.04631.497.2

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Processing

Software
NameVersionClassification
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.6model building
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LEZ

4lez


Resolution: 2.57→28.92 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 22.048 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.651 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 1716 4.8 %RANDOM
Rwork0.1957 ---
obs0.1979 33857 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 191.4 Å2 / Biso mean: 65.737 Å2 / Biso min: 27.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0 Å20 Å2
2---0 Å20 Å2
3----1.08 Å2
Refinement stepCycle: final / Resolution: 2.57→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 1464 132 47 7330
Biso mean--58.69 42.66 -
Num. residues----758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0167675
X-RAY DIFFRACTIONr_bond_other_d0.0010.026537
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.72310568
X-RAY DIFFRACTIONr_angle_other_deg1.1052.7715201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19222.516306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.137151159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6381535
X-RAY DIFFRACTIONr_chiral_restr0.0710.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021660
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.571→2.638 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 125 -
Rwork0.272 2307 -
all-2432 -
obs--93.11 %
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)
12.031-0.566-0.14622.58730.01521.4260.0115-0.18960.24970.16710.00790.1921-0.2096-0.1794-0.01940.07380.0284-0.00270.048-0.04180.12015.39527.40420.013
22.1902-0.89970.28392.9088-0.7191.7343-0.0723-0.2654-0.27510.0550.0299-0.29470.29150.22180.04240.09080.05560.02730.0950.06130.187333.448-8.23518.467
35.3157-0.91691.38262.9432.56285.53740.0964-1.0702-0.10560.77340.0510.05360.50240.1686-0.14750.3114-0.15920.02190.38-0.0330.193429.09823.14731.696
44.3509-0.4841.19343.7084-1.15787.95660.1956-0.8099-0.05870.63160.0286-0.08210.37120.46-0.22420.2307-0.0028-0.06410.2466-0.0770.159129.77523.70832.225
54.1987-1.9976-1.28784.8264-1.77562.15710.08420.3022-0.4382-0.17770.08740.350.127-0.4862-0.17160.1648-0.13340.01930.30550.08970.31638.289-8.58717.789
66.1177-0.45180.13797.14271.43515.37580.14020.6575-0.3836-0.38930.12670.3276-0.123-0.4988-0.26690.14590.03140.06810.22880.12420.25238.621-6.80818.356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A147 - 507
2X-RAY DIFFRACTION2C149 - 507
3X-RAY DIFFRACTION3E1 - 18
4X-RAY DIFFRACTION4F1 - 18
5X-RAY DIFFRACTION5I1 - 18
6X-RAY DIFFRACTION6J1 - 18

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