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- PDB-7utt: Structure of Non-hydrolyzable ATP (ApCpp) binds to Cyclic GMP AMP... -

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Basic information

Entry
Database: PDB / ID: 7utt
TitleStructure of Non-hydrolyzable ATP (ApCpp) binds to Cyclic GMP AMP synthase (cGAS) through Mn coordination
Components
  • Cyclic GMP-AMP synthase
  • Palindromic DNA18
KeywordsTransferase/DNA / non-hydrolyzable ATP (ApCpp) / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / 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: 2.04 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 Non-hydrolyzable ATP (ApCpp) binds to Cyclic GMP AMP synthase (cGAS) through Mn coordination
Authors: Wu, S. / Gabelli, S.B. / Sohn, J.S.
History
DepositionApr 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 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)108,70014
Polymers107,3396
Non-polymers1,3618
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, As a non-hydrolyzable ATP, ApCpp can interact with cGAS. Divalent metal Mn (or Mg) coordinates ApCpp tri-phosphate to negative charged catalytic residues. ...Evidence: isothermal titration calorimetry, As a non-hydrolyzable ATP, ApCpp can interact with cGAS. Divalent metal Mn (or Mg) coordinates ApCpp tri-phosphate to negative charged catalytic residues. Zn is involved in Zink finger formation at the cGAS dimer interface.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-72 kcal/mol
Surface area41510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.093, 97.882, 142.271
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
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: isolated from a genetically manipulated source
Details: ordered from IDT / Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others)

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Non-polymers , 4 types, 318 molecules

#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#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 / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.5 Å3/Da / Density % sol: 50.81 % / 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: 0.9793 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: 2.04→29.67 Å / Num. obs: 69038 / % possible obs: 99 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Net I/σ(I): 11.1
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
2.04-2.085.70.7282141337620.7450.3260.82.384.7
9.76-29.665.80.04940787070.9960.0220.05425.196.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.6model building
PDB_EXTRACTV3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LEZ

4lez


Resolution: 2.04→29.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.214 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.146 / 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
Rfree0.2104 2000 2.9 %RANDOM
Rwork0.1811 ---
obs0.1819 66963 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.54 Å2 / Biso mean: 46.58 Å2 / Biso min: 19.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.38 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 2.04→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5759 1464 68 310 7601
Biso mean--31.59 39.8 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0167677
X-RAY DIFFRACTIONr_bond_other_d0.0010.026574
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.73210537
X-RAY DIFFRACTIONr_angle_other_deg1.1972.77815286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0575691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2722.588313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.931151178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7231536
X-RAY DIFFRACTIONr_chiral_restr0.0880.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021668
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: 2.04→2.09 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.278 133 -
Rwork0.243 4437 -
obs--90.37 %
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)
11.21140.1703-0.26321.28720.01741.030.01270.12730.1838-0.0390-0.1242-0.11270.0786-0.01280.0268-0.0054-0.00490.04630.020.0684-4.98726.72-20.404
21.26070.49980.11842.09530.52360.823-0.06840.1726-0.04840.02730.00930.37780.0758-0.09720.05910.0402-0.03460.03520.0967-0.01450.1233-33.471-8.676-18.898
33.18160.68371.17752.2189-0.7393.78550.1380.6737-0.0137-0.39430.01650.04050.2647-0.114-0.15450.0960.0617-0.0020.23240.03920.1381-28.61922.399-31.846
42.96170.3580.52741.7615-0.08014.36940.22810.4495-0.0541-0.27170.0383-0.00850.1943-0.2229-0.26630.14320.0111-0.02780.24070.04630.1871-29.27222.968-32.31
53.11621.3804-1.06974.4370.50190.87390.1264-0.1454-0.27110.20590.0222-0.28690.0310.3199-0.14860.07410.0401-0.02520.3152-0.13030.2219-8.364-8.605-17.671
63.22340.6847-1.46584.8937-0.45662.8860.0355-0.34-0.06580.32560.1165-0.354-0.04930.3802-0.15210.0920.0052-0.00120.1555-0.10630.1802-8.576-6.982-18.306
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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