+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17667 | |||||||||
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Title | cA4-bound Cami1 in complex with 70S ribosome | |||||||||
Map data | Sharpened composite map | |||||||||
Sample |
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Keywords | CRISPR / cyclic oligoadenylate / RNAse / RelE-toxin / HYDROLASE / RIBOSOME | |||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) / Streptococcus thermophilus (bacteria) / Allochromatium vinosum (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.67 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_17667.map.gz | 228.3 MB | EMDB map data format | |
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Header (meta data) | emd-17667-v30.xml emd-17667.xml | 82.3 KB 82.3 KB | Display Display | EMDB header |
Images | emd_17667.png | 84.6 KB | ||
Filedesc metadata | emd-17667.cif.gz | 15.4 KB | ||
Others | emd_17667_additional_1.map.gz | 116.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17667 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17667 | HTTPS FTP |
-Related structure data
Related structure data | 8phjMC 8phbC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17667.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened composite map | ||||||||||||||||||||
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
-Additional map: Unsharpened composite map
File | emd_17667_additional_1.map | ||||||||||||
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Annotation | Unsharpened composite map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cami1 bound in 70S E.coli ribosome
+Supramolecule #1: Cami1 bound in 70S E.coli ribosome
+Supramolecule #2: 70S E.coli ribosome
+Supramolecule #3: synthetic mRNA
+Supramolecule #4: cA4
+Supramolecule #5: CRISPR-associated protein Cami1, APE2256 family
+Macromolecule #1: Large ribosomal subunit protein bL33
+Macromolecule #2: Large ribosomal subunit protein bL34
+Macromolecule #3: Large ribosomal subunit protein bL35
+Macromolecule #4: Large ribosomal subunit protein bL36A
+Macromolecule #5: Large ribosomal subunit protein bL31A
+Macromolecule #6: Large ribosomal subunit protein uL10
+Macromolecule #7: Large ribosomal subunit protein uL11
+Macromolecule #11: Small ribosomal subunit protein uS2
+Macromolecule #12: Small ribosomal subunit protein uS3
+Macromolecule #13: Small ribosomal subunit protein uS4
+Macromolecule #14: Small ribosomal subunit protein uS5
+Macromolecule #15: Small ribosomal subunit protein bS6, fully modified isoform
+Macromolecule #16: Small ribosomal subunit protein uS7
+Macromolecule #17: Small ribosomal subunit protein uS8
+Macromolecule #18: Small ribosomal subunit protein uS9
+Macromolecule #19: Small ribosomal subunit protein uS10
+Macromolecule #20: Small ribosomal subunit protein uS11
+Macromolecule #21: Small ribosomal subunit protein uS12
+Macromolecule #22: Small ribosomal subunit protein uS13
+Macromolecule #23: Small ribosomal subunit protein uS14
+Macromolecule #24: Small ribosomal subunit protein uS15
+Macromolecule #25: Small ribosomal subunit protein bS16
+Macromolecule #26: Small ribosomal subunit protein uS17
+Macromolecule #27: Small ribosomal subunit protein bS18
+Macromolecule #28: Small ribosomal subunit protein uS19
+Macromolecule #29: Small ribosomal subunit protein bS20
+Macromolecule #30: Small ribosomal subunit protein bS21
+Macromolecule #31: Large ribosomal subunit protein bL12
+Macromolecule #32: CRISPR-associated protein, APE2256 family
+Macromolecule #35: Large ribosomal subunit protein uL2
+Macromolecule #36: Large ribosomal subunit protein uL3
+Macromolecule #37: Large ribosomal subunit protein uL4
+Macromolecule #38: Large ribosomal subunit protein uL5
+Macromolecule #39: Large ribosomal subunit protein uL6
+Macromolecule #40: Large ribosomal subunit protein bL9
+Macromolecule #41: Large ribosomal subunit protein uL13
+Macromolecule #42: Large ribosomal subunit protein uL14
+Macromolecule #43: Large ribosomal subunit protein uL15
+Macromolecule #44: Large ribosomal subunit protein uL16
+Macromolecule #45: Large ribosomal subunit protein bL17
+Macromolecule #46: Large ribosomal subunit protein uL18
+Macromolecule #47: Large ribosomal subunit protein bL19
+Macromolecule #48: Large ribosomal subunit protein bL20
+Macromolecule #49: Large ribosomal subunit protein bL21
+Macromolecule #50: Large ribosomal subunit protein uL22
+Macromolecule #51: Large ribosomal subunit protein uL23
+Macromolecule #52: Large ribosomal subunit protein uL24
+Macromolecule #53: Large ribosomal subunit protein bL25
+Macromolecule #54: Large ribosomal subunit protein bL27
+Macromolecule #55: Large ribosomal subunit protein bL28
+Macromolecule #56: Large ribosomal subunit protein uL29
+Macromolecule #57: Large ribosomal subunit protein uL30
+Macromolecule #58: Large ribosomal subunit protein bL32
+Macromolecule #8: fMet-tRNA(fMet)
+Macromolecule #9: mRNA
+Macromolecule #10: 16S rRNA
+Macromolecule #33: 23S rRNA (2862-MER)
+Macromolecule #34: 5S rRNA
+Macromolecule #59: Cyclic tetraadenosine monophosphate (cA4)
+Macromolecule #60: ZINC ION
+Macromolecule #61: MAGNESIUM ION
-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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Grid | Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Details: GLOW DISCHARGED 60 seconds |
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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: OTHER Details: Composite map, resolution determined by the local refimenet map of lowest resolution Number images used: 158387 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |