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- PDB-7v0w: Structure of Ternary Complex of cGAS with dsDNA and Bound 5 -pppG... -

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Basic information

Entry
Database: PDB / ID: 7v0w
TitleStructure of Ternary Complex of cGAS with dsDNA and Bound 5 -pppG(2,5 )pA
Components
  • Cyclic GMP-AMP synthase
  • Palindromic DNA18
KeywordsTransferase/DNA / 5 -pppG(2 / 5 )pA / 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
ADENOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / 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: 2.66 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 Ternary Complex of cGAS with dsDNA and Bound 5 -pppG(2 ,5 )pA
Authors: Wu, S. / Gabelli, S.B. / Sohn, J.S.
History
DepositionMay 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 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)109,31614
Polymers107,3356
Non-polymers1,9818
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-61 kcal/mol
Surface area40530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.475, 99.474, 142.088
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: obtained synthetically / Source: (synth.) Synthetic Construct (others)

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Non-polymers , 5 types, 32 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A / ADENOSINE-5'-MONOPHOSPHATE / Adenosine monophosphate


Type: RNA linking / Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.58 Å3/Da / Density % sol: 52.39 % / Description: 0.3mm, polarizes nicely
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-1 / Wavelength: 1.8785 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: 1.8785 Å / Relative weight: 1
ReflectionResolution: 2.66→28.91 Å / Num. obs: 32675 / % possible obs: 99.5 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.038 / Rrim(I) all: 0.096 / Net I/σ(I): 11.6 / Num. measured all: 212442 / Scaling rejects: 1
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
2.66-2.796.30.6282646642060.8650.2670.6842.597.8
8.81-28.916.20.06761219810.9930.0310.07424.297.1

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Processing

Software
NameVersionClassification
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
REFMAC5.8.0267refinement
PDB-REDO7.37refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lez

4lez


Resolution: 2.66→28.91 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 25.646 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 1.053 / ESU R Free: 0.313 / 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
Rfree0.2384 1642 5 %RANDOM
Rwork0.1991 ---
obs0.201 30977 99.48 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 181.23 Å2 / Biso mean: 80.043 Å2 / Biso min: 35.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0 Å2
2---0.25 Å20 Å2
3---0.46 Å2
Refinement stepCycle: final / Resolution: 2.66→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5668 1464 112 24 7268
Biso mean--65.18 53 -
Num. residues----756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0167635
X-RAY DIFFRACTIONr_bond_other_d0.0020.026521
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.71310492
X-RAY DIFFRACTIONr_angle_other_deg1.1412.76915154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.222.476307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66151159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2931536
X-RAY DIFFRACTIONr_chiral_restr0.0770.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027198
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021664
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: 2.66→2.725 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.334 110 -
Rwork0.33 2169 -
obs--96.12 %
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)
12.04990.975-0.32473.3592-0.00991.6074-0.06060.14470.1447-0.41380.025-0.371-0.27590.24720.03560.1708-0.03780.0370.09280.05720.1026-5.54427.551-20.173
22.65261.4260.41413.59140.42861.723-0.16140.2611-0.2568-0.32290.06680.16620.2875-0.2160.09460.1617-0.03680.03760.0826-0.03830.0763-33.55-7.947-19.02
34.28050.17232.06351.6856-1.90074.06870.08230.7061-0.1704-0.42130.131-0.08610.0515-0.1292-0.21330.59540.23110.07470.30550.05150.1519-29.35523.673-31.851
42.71220.56132.52362.9594-1.90026.53540.22270.4665-0.0763-0.4681-0.0375-0.11890.7889-0.4232-0.18520.32350.0253-0.0310.55020.03340.1364-29.94224.196-32.279
54.13051.7235-3.3335.03510.69764.8999-0.186-0.3575-0.6788-0.0690.0855-0.33410.41780.69890.10060.30590.24790.09240.2780.06840.3999-8.361-8.587-18.377
66.53770.5940.13596.254-2.21846.8118-0.0425-0.7034-0.52630.08210.1692-0.5584-0.15010.6846-0.12670.2850.05460.15530.2702-0.05910.3019-8.778-6.884-18.779
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A149 - 506
2X-RAY DIFFRACTION2C149 - 506
3X-RAY DIFFRACTION3E1 - 18
4X-RAY DIFFRACTION4F1 - 18
5X-RAY DIFFRACTION5I1 - 18
6X-RAY DIFFRACTION6J1 - 18

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