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

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Basic information

Entry
Database: PDB / ID: 7uzr
TitleStructure of Ternary Complex of cGAS with dsDNA and Bound 5 -pppG(2 ,5 )pG
Components
  • Cyclic GMP-AMP synthase
  • Palindromic DNA18
KeywordsTRANSFERASE/DNA / Complex / pppGpG / Manganese / IMMUNE SYSTEM / TRANSFERASE-DNA complex
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of type I interferon production / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway / negative regulation of DNA repair ...2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of type I interferon production / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway / negative regulation of DNA repair / cGMP-mediated signaling / cellular response to exogenous dsRNA / positive regulation of type I interferon production / nucleosome binding / regulation of immune response / negative regulation of double-strand break repair via homologous recombination / 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-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / Mab-21 protein nucleotidyltransferase domain
Similarity search - Domain/homology
: / Chem-OKR / 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: 2.7 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: 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
DepositionMay 9, 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
Revision 1.2May 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 / _citation_author.identifier_ORCID / _citation_author.name

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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)109,42614
Polymers107,3396
Non-polymers2,0878
Water37821
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 area10110 Å2
ΔGint-65 kcal/mol
Surface area41480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.534, 99.000, 143.091
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: 42640.254 Da / Num. of mol.: 2 / Fragment: catalytic domain, 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: 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 , 4 types, 29 molecules

#3: Chemical ChemComp-OKR / [[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 868.386 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N10O21P4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.59 Å3/Da / Density % sol: 52.53 % / 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-2 / Wavelength: 0.979338 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: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.7→29.76 Å / Num. obs: 31191 / % possible obs: 98.9 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.048 / Rrim(I) all: 0.123 / Net I/σ(I): 10.6 / Num. measured all: 206002 / 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
2.7-2.836.30.9132400838030.7230.3870.993292.6
8.94-29.765.90.03955449410.9980.0170.04328.697.3

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Processing

Software
NameVersionClassification
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.6model building
REFMAC5.8.0267refinement
PDB-REDO7.37refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LEZ

4lez


Resolution: 2.7→29.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 30.015 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 3.215 / ESU R Free: 0.336 / 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
Rfree0.2447 1545 5 %RANDOM
Rwork0.1893 ---
obs0.1922 29565 98.8 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 193.91 Å2 / Biso mean: 71.736 Å2 / Biso min: 23.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å2-0 Å2
2--0.07 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 2.7→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5742 1464 116 21 7343
Biso mean--67.96 41.1 -
Num. residues----765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0167714
X-RAY DIFFRACTIONr_bond_other_d0.0020.026579
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.72210600
X-RAY DIFFRACTIONr_angle_other_deg1.162.77115295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4385687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27322.532312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.566151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9351536
X-RAY DIFFRACTIONr_chiral_restr0.0840.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021679
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: 2.7→2.766 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.327 96 -
Rwork0.313 1872 -
obs--85.71 %
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)
12.24290.8929-0.32413.4977-0.39481.693-0.07710.19660.2276-0.33040.022-0.3444-0.18490.22620.05510.1222-0.03510.00470.05670.03550.0929-5.05427.415-20.457
22.77931.74480.24014.28730.58021.6625-0.27870.3978-0.2425-0.41380.22050.2470.2156-0.25270.05820.1521-0.07940.05010.1086-0.0370.1156-33.633-8.202-19.038
35.44630.89592.67671.988-1.75084.716-0.04930.8307-0.1825-0.45880.2548-0.1022-0.0816-0.2255-0.20550.57520.32740.13310.43540.09620.1443-29.2923.342-32.016
43.85320.37322.15793.27050.27117.5350.30380.651-0.0244-0.268-0.0608-0.08770.4921-0.5381-0.2430.17660.0168-0.03040.25750.07030.1192-29.89823.906-32.446
55.72842.708-3.20195.88641.21883.4721-0.1382-0.4009-0.68670.084-0.0023-0.50270.21130.42390.14040.25830.19770.01150.2079-0.07130.4195-8.386-8.504-18.228
66.14420.7671-0.40867.1642-2.83787.2544-0.1172-0.4611-0.67440.27320.0341-0.8172-0.07570.6620.08310.2909-0.00530.13090.2082-0.10130.3502-8.729-6.841-18.622
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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