+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42967 | |||||||||
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Title | CryoEM structure of AriA-AriB complex (Form II) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Bacterial Defense system / Toxin-antitoxin system / AriAB / PARIS / IMMUNE SYSTEM | |||||||||
Function / homology | : / : Function and homology information | |||||||||
Biological species | Escherichia coli B185 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.08 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_42967.map.gz | 107.5 MB | EMDB map data format | |
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Header (meta data) | emd-42967-v30.xml emd-42967.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42967_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_42967.png | 119.2 KB | ||
Filedesc metadata | emd-42967.cif.gz | 6.1 KB | ||
Others | emd_42967_half_map_1.map.gz emd_42967_half_map_2.map.gz | 200.2 MB 200.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42967 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42967 | HTTPS FTP |
-Validation report
Summary document | emd_42967_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_42967_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_42967_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_42967_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42967 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42967 | HTTPS FTP |
-Related structure data
Related structure data | 8v47MC 8v45C 8v46C 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_42967.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-Half map: #2
File | emd_42967_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_42967_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : AriAB complex
Entire | Name: AriAB complex |
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Components |
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-Supramolecule #1: AriAB complex
Supramolecule | Name: AriAB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: AriA-AriB |
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Source (natural) | Organism: Escherichia coli B185 (bacteria) |
Molecular weight | Theoretical: 360 KDa |
-Macromolecule #1: AriA antitoxin
Macromolecule | Name: AriA antitoxin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli B185 (bacteria) |
Molecular weight | Theoretical: 53.287113 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 AIVLIDQPEI SLHI DWQED LLKRMLSQLS GRQIIVCTHS PSIATGYEDF MINISPEFIS SRDNDNHKDS EEMEEDESL UniProtKB: UNIPROTKB: D6IC77 |
-Macromolecule #2: AriB
Macromolecule | Name: AriB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli B185 (bacteria) |
Molecular weight | Theoretical: 34.749578 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSSCAYTIDS YITLLTMSSK KRLLVEGRHD RSHLYQLIYK FNPASKVKID TAQDIKASDK AMSKNNRLKI ETIHSKVKGK DNISFLCDR AFREFAFNDQ IEDLLNSHYC DDSLYWTLGH SLENYFFNPS IIIDAFQFLS PSEYKYKAIE LFSELISSSF A VLAAVSLA ...String: MSSCAYTIDS YITLLTMSSK KRLLVEGRHD RSHLYQLIYK FNPASKVKID TAQDIKASDK AMSKNNRLKI ETIHSKVKGK DNISFLCDR AFREFAFNDQ IEDLLNSHYC DDSLYWTLGH SLENYFFNPS IIIDAFQFLS PSEYKYKAIE LFSELISSSF A VLAAVSLA AKDIDKAGLP AALIDWKDIV INDGTIKLIR RDSYDIDSAC VDSFFNAFDA VLPRVIASDV GICSRVVRGH TG ILLLQKL FSACLYYVGR EDDALQADSS ANYFCNLSEL SLTTALAESW VRKIGVLEDV YFPDSLLKNI E UniProtKB: UNIPROTKB: D6IC76 |
-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 |
-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: 5058 / 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: 2.2 µm / Nominal defocus min: 0.8 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-8v47: |