+Open data
-Basic information
Entry | Database: PDB / ID: 8bto | ||||||
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Title | Helical structure of BcThsA in complex with 1''-3'gcADPR | ||||||
Components | NAD(+) hydrolase ThsA | ||||||
Keywords | HYDROLASE / Thoeris / SIR2 domain / SLOG domain / 3'cADPR | ||||||
Function / homology | Function and homology information NAD+ glycohydrolase / defense response to virus / hydrolase activity / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus cereus MSX-D12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.96 Å | ||||||
Authors | Tamulaitiene, G. / Sasnauskas, G. / Sabonis, D. | ||||||
Funding support | Lithuania, 1items
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Citation | Journal: Nature / Year: 2024 Title: Activation of Thoeris antiviral system via SIR2 effector filament assembly. Authors: Giedre Tamulaitiene / Dziugas Sabonis / Giedrius Sasnauskas / Audrone Ruksenaite / Arunas Silanskas / Carmel Avraham / Gal Ofir / Rotem Sorek / Mindaugas Zaremba / Virginijus Siksnys / Abstract: To survive bacteriophage (phage) infections, bacteria developed numerous anti-phage defence systems. Some of them (for example, type III CRISPR-Cas, CBASS, Pycsar and Thoeris) consist of two modules: ...To survive bacteriophage (phage) infections, bacteria developed numerous anti-phage defence systems. Some of them (for example, type III CRISPR-Cas, CBASS, Pycsar and Thoeris) consist of two modules: a sensor responsible for infection recognition and an effector that stops viral replication by destroying key cellular components. In the Thoeris system, a Toll/interleukin-1 receptor (TIR)-domain protein, ThsB, acts as a sensor that synthesizes an isomer of cyclic ADP ribose, 1''-3' glycocyclic ADP ribose (gcADPR), which is bound in the Smf/DprA-LOG (SLOG) domain of the ThsA effector and activates the silent information regulator 2 (SIR2)-domain-mediated hydrolysis of a key cell metabolite, NAD (refs. ). Although the structure of ThsA has been solved, the ThsA activation mechanism remained incompletely understood. Here we show that 1''-3' gcADPR, synthesized in vitro by the dimeric ThsB' protein, binds to the ThsA SLOG domain, thereby activating ThsA by triggering helical filament assembly of ThsA tetramers. The cryogenic electron microscopy (cryo-EM) structure of activated ThsA revealed that filament assembly stabilizes the active conformation of the ThsA SIR2 domain, enabling rapid NAD depletion. Furthermore, we demonstrate that filament formation enables a switch-like response of ThsA to the 1''-3' gcADPR signal. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bto.cif.gz | 980.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bto.ent.gz | 818.9 KB | Display | PDB format |
PDBx/mmJSON format | 8bto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bto_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 8bto_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8bto_validation.xml.gz | 159.4 KB | Display | |
Data in CIF | 8bto_validation.cif.gz | 233 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/8bto ftp://data.pdbj.org/pub/pdb/validation_reports/bt/8bto | HTTPS FTP |
-Related structure data
Related structure data | 16233MC 8btnC 8btpC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 55417.746 Da / Num. of mol.: 12 / Mutation: N112A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus MSX-D12 (bacteria) / Gene: thsA, II9_05448 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J8G6Z1, NAD+ glycohydrolase #2: Chemical | ChemComp-OJC / ( #3: Chemical | ChemComp-NAD / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: BcThsA in complex with 1''-3'gcADPR / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: Bacillus cereus (bacteria) | ||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 46.33 sec. / Electron dose: 30.64 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2321 |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 128.947 ° / Axial rise/subunit: 41.87 Å / Axial symmetry: D2 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 233008 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.29 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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