+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17666 | |||||||||
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Title | Cami1-ribosome local refinement map with mask on 50S subunit | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CRISPR / cyclic oligoadenylate / RNAse / RelE-toxin / RIBOSOME | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Tamulaitiene G / Mogila I / Sasnauskas G / Tamulaitis G | |||||||||
Funding support | Lithuania, 1 items
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Citation | Journal: Science / Year: 2023 Title: Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling. Authors: Irmantas Mogila / Giedre Tamulaitiene / Konstanty Keda / Albertas Timinskas / Audrone Ruksenaite / Giedrius Sasnauskas / Česlovas Venclovas / Virginijus Siksnys / Gintautas Tamulaitis Abstract: Prokaryotic type III CRISPR-Cas antiviral systems employ cyclic oligoadenylate (cA) signaling to activate a diverse range of auxiliary proteins that reinforce the CRISPR-Cas defense. Here we ...Prokaryotic type III CRISPR-Cas antiviral systems employ cyclic oligoadenylate (cA) signaling to activate a diverse range of auxiliary proteins that reinforce the CRISPR-Cas defense. Here we characterize a class of cA-dependent effector proteins named CRISPR-Cas-associated messenger RNA (mRNA) interferase 1 (Cami1) consisting of a CRISPR-associated Rossmann fold sensor domain fused to winged helix-turn-helix and a RelE-family mRNA interferase domain. Upon activation by cyclic tetra-adenylate (cA), Cami1 cleaves mRNA exposed at the ribosomal A-site thereby depleting mRNA and leading to cell growth arrest. The structures of apo-Cami1 and the ribosome-bound Cami1-cA complex delineate the conformational changes that lead to Cami1 activation and the mechanism of Cami1 binding to a bacterial ribosome, revealing unexpected parallels with eukaryotic ribosome-inactivating proteins. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17666.map.gz | 123.1 MB | EMDB map data format | |
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Header (meta data) | emd-17666-v30.xml emd-17666.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17666_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_17666.png | 75.6 KB | ||
Masks | emd_17666_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-17666.cif.gz | 4 KB | ||
Others | emd_17666_half_map_1.map.gz emd_17666_half_map_2.map.gz | 227 MB 227 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17666 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17666 | HTTPS FTP |
-Validation report
Summary document | emd_17666_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_17666_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_17666_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | emd_17666_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17666 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17666 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17666.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17666_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17666_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17666_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cami1 bound in 70S E.coli ribosome
Entire | Name: Cami1 bound in 70S E.coli ribosome |
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Components |
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-Supramolecule #1: Cami1 bound in 70S E.coli ribosome
Supramolecule | Name: Cami1 bound in 70S E.coli ribosome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |