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- PDB-7uxs: Crystal structure of the BcThsA SLOG domain in complex with 3'cADPR -

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Basic information

Entry
Database: PDB / ID: 7uxs
TitleCrystal structure of the BcThsA SLOG domain in complex with 3'cADPR
ComponentsBcThsA
KeywordsHYDROLASE / cADPR isomer / bacterial TIR / Thoeris defense system / ThsA / ThsB / antiphage defense / NAD+
Function / homologyChem-OJC
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsShi, Y. / Masic, V. / Mosaiab, T. / Ve, T.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Science / Year: 2022
Title: Cyclic ADP ribose isomers: Production, chemical structures, and immune signaling.
Authors: Mohammad K Manik / Yun Shi / Sulin Li / Mark A Zaydman / Neha Damaraju / Samuel Eastman / Thomas G Smith / Weixi Gu / Veronika Masic / Tamim Mosaiab / James S Weagley / Steven J Hancock / ...Authors: Mohammad K Manik / Yun Shi / Sulin Li / Mark A Zaydman / Neha Damaraju / Samuel Eastman / Thomas G Smith / Weixi Gu / Veronika Masic / Tamim Mosaiab / James S Weagley / Steven J Hancock / Eduardo Vasquez / Lauren Hartley-Tassell / Nestoras Kargios / Natsumi Maruta / Bryan Y J Lim / Hayden Burdett / Michael J Landsberg / Mark A Schembri / Ivan Prokes / Lijiang Song / Murray Grant / Aaron DiAntonio / Jeffrey D Nanson / Ming Guo / Jeffrey Milbrandt / Thomas Ve / Bostjan Kobe /
Abstract: Cyclic adenosine diphosphate (ADP)-ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide ...Cyclic adenosine diphosphate (ADP)-ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide (oxidized form) (NAD) hydrolysis. We show that v-cADPR (2'cADPR) and v2-cADPR (3'cADPR) isomers are cyclized by O-glycosidic bond formation between the ribose moieties in ADPR. Structures of 2'cADPR-producing TIR domains reveal conformational changes that lead to an active assembly that resembles those of Toll-like receptor adaptor TIR domains. Mutagenesis reveals a conserved tryptophan that is essential for cyclization. We show that 3'cADPR is an activator of ThsA effector proteins from the bacterial antiphage defense system termed Thoeris and a suppressor of plant immunity when produced by the effector HopAM1. Collectively, our results reveal the molecular basis of cADPR isomer production and establish 3'cADPR in bacteria as an antiviral and plant immunity-suppressing signaling molecule.
History
DepositionMay 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 12, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 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

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Assembly

Deposited unit
B: BcThsA
A: BcThsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0637
Polymers44,7002
Non-polymers1,3635
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-20 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.194, 70.801, 121.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein BcThsA


Mass: 22350.076 Da / Num. of mol.: 2 / Fragment: SLOG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-OJC / (2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione


Mass: 541.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N5O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris, pH 5.5, 0.1 M ammonium sulfate, 25-29% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.57→46.16 Å / Num. obs: 56724 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 15.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.016 / Rrim(I) all: 0.042 / Net I/σ(I): 20.2
Reflection shellResolution: 1.57→1.59 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 2652 / CC1/2: 0.97 / Rpim(I) all: 0.102 / Rrim(I) all: 0.264 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6LHX

6lhx


Resolution: 1.57→36.87 Å / SU ML: 0.1435 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.2414
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1763 2000 3.53 %
Rwork0.1488 54645 -
obs0.1497 56645 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.84 Å2
Refinement stepCycle: LAST / Resolution: 1.57→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 87 365 3596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833312
X-RAY DIFFRACTIONf_angle_d0.94534487
X-RAY DIFFRACTIONf_chiral_restr0.0546481
X-RAY DIFFRACTIONf_plane_restr0.0098600
X-RAY DIFFRACTIONf_dihedral_angle_d13.72841249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.20621360.17713720X-RAY DIFFRACTION96.59
1.61-1.650.18971430.15323881X-RAY DIFFRACTION100
1.65-1.70.18831400.14853827X-RAY DIFFRACTION99.9
1.7-1.750.16621400.14563856X-RAY DIFFRACTION99.97
1.75-1.820.18511430.14153889X-RAY DIFFRACTION100
1.82-1.890.17041410.14453860X-RAY DIFFRACTION100
1.89-1.980.16221430.14953892X-RAY DIFFRACTION99.93
1.98-2.080.16121420.14093890X-RAY DIFFRACTION99.98
2.08-2.210.181430.1393901X-RAY DIFFRACTION100
2.21-2.380.17681410.14213887X-RAY DIFFRACTION99.93
2.38-2.620.17321440.14973932X-RAY DIFFRACTION99.9
2.62-30.17141460.14973949X-RAY DIFFRACTION99.9
3-3.780.16581450.14793985X-RAY DIFFRACTION99.98
3.78-36.870.19111530.15574176X-RAY DIFFRACTION99.72

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