+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42965 | |||||||||
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Title | CryoEM structure of AriA-Ocr complex | |||||||||
Map data | Main map | |||||||||
Sample |
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Keywords | Bacterial Defense system / Toxin-antitoxin system / AriAB / PARIS / Immune system | |||||||||
Function / homology | B-form DNA mimic Ocr / DNA mimic ocr / Protein Ocr / symbiont-mediated evasion of host restriction-modification system / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / : / Protein Ocr Function and homology information | |||||||||
Biological species | Escherichia coli B185 (bacteria) / Escherichia phage T7 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.63 Å | |||||||||
Authors | Deep A / Corbett KD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2024 Title: Architecture and activation mechanism of the bacterial PARIS defence system. Authors: Amar Deep / Qishan Liang / Eray Enustun / Joe Pogliano / Kevin D Corbett / Abstract: Bacteria and their viruses (bacteriophages or phages) are engaged in an intense evolutionary arms race. While the mechanisms of many bacterial antiphage defence systems are known, how these systems ...Bacteria and their viruses (bacteriophages or phages) are engaged in an intense evolutionary arms race. While the mechanisms of many bacterial antiphage defence systems are known, how these systems avoid toxicity outside infection yet activate quickly after infection is less well understood. Here we show that the bacterial phage anti-restriction-induced system (PARIS) operates as a toxin-antitoxin system, in which the antitoxin AriA sequesters and inactivates the toxin AriB until triggered by the T7 phage counterdefence protein Ocr. Using cryo-electron microscopy, we show that AriA is related to SMC-family ATPases but assembles into a distinctive homohexameric complex through two oligomerization interfaces. In uninfected cells, the AriA hexamer binds to up to three monomers of AriB, maintaining them in an inactive state. After Ocr binding, the AriA hexamer undergoes a structural rearrangement, releasing AriB and allowing it to dimerize and activate. AriB is a toprim/OLD-family nuclease, the activation of which arrests cell growth and inhibits phage propagation by globally inhibiting protein translation through specific cleavage of a lysine tRNA. Collectively, our findings reveal the intricate molecular mechanisms of a bacterial defence system triggered by a phage counterdefence protein, and highlight how an SMC-family ATPase has been adapted as a bacterial infection sensor. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42965.map.gz | 62.4 MB | EMDB map data format | |
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Header (meta data) | emd-42965-v30.xml emd-42965.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42965_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_42965.png | 110.2 KB | ||
Filedesc metadata | emd-42965.cif.gz | 6.3 KB | ||
Others | emd_42965_additional_1.map.gz emd_42965_half_map_1.map.gz emd_42965_half_map_2.map.gz | 62.6 MB 116.2 MB 116.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42965 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42965 | HTTPS FTP |
-Validation report
Summary document | emd_42965_validation.pdf.gz | 971.1 KB | Display | EMDB validaton report |
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Full document | emd_42965_full_validation.pdf.gz | 970.7 KB | Display | |
Data in XML | emd_42965_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | emd_42965_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42965 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42965 | HTTPS FTP |
-Related structure data
Related structure data | 8v45MC 8v46C 8v47C 8v48C 8v49C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42965.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.935 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Local Refinement map
File | emd_42965_additional_1.map | ||||||||||||
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Annotation | Local Refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_42965_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_42965_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : AriA hexamer with two monomers of Ocr
Entire | Name: AriA hexamer with two monomers of Ocr |
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Components |
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-Supramolecule #1: AriA hexamer with two monomers of Ocr
Supramolecule | Name: AriA hexamer with two monomers of Ocr / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: AriA(6)-Ocr(2) |
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Source (natural) | Organism: Escherichia coli B185 (bacteria) |
-Macromolecule #1: AriA antitoxin
Macromolecule | Name: AriA antitoxin / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli B185 (bacteria) |
Molecular weight | Theoretical: 53.288098 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: VAIRTISKIE LSKIHNRYNL TVDFFNDLNV IHGKNGAGKS TLIHVIANIV NGDFIRFAFL IFEEIKATYS DGLKIVIRRD KIDEQSFIS VTLSNGKYIK FAVGEAMATV REIESERHLR ERDVKSMLAM DIDKFVKENE LQKVRASYFP AFRTMLEAWS S SSDVGYER ...String: VAIRTISKIE LSKIHNRYNL TVDFFNDLNV IHGKNGAGKS TLIHVIANIV NGDFIRFAFL IFEEIKATYS DGLKIVIRRD KIDEQSFIS VTLSNGKYIK FAVGEAMATV REIESERHLR ERDVKSMLAM DIDKFVKENE LQKVRASYFP AFRTMLEAWS S SSDVGYER RVIRSSFYNR KASAFARELF GQFLPSINYP SPMEIEDRLR EEIRRAQLGI AAYESRTFSE SFVKVFSALF DN SSVEGEI TGELLKEIEG LAIAQDSSIK NGYYAEYSKV YEEIRSLINR NLKGKVENSV SGALVVYRDA LRDRQDYQEK AFS EIDNYM SSVNSFLEDK EMAYDFDLRR KYPKVGLKFP DGSWSPIRVL SSGERQLLTM LYAASKMGDD AIVLIDEPEI SLHI DWQED LLKRMLSQLS GRQIIVCTHS PSIATGYEDF MINISPEFIS SRDNDNHKDS EEMEEDESL UniProtKB: UNIPROTKB: D6IC77 |
-Macromolecule #2: Protein Ocr
Macromolecule | Name: Protein Ocr / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage T7 (virus) |
Molecular weight | Theoretical: 13.819015 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAMSNMTYNN VFDHAYEMLK ENIRYDDIRD TDDLHDAIHM AADNAVPHYY ADIFSVMASE GIDLEFEDSG LMPDTKDVIR ILQARIYEQ LTIDLWEDAE DLLNEYLEEV EEYEEDEE UniProtKB: Protein Ocr |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 12 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | Sample was a mixture of three proteins. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 6821 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8v45: |