+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13955 | |||||||||
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Title | Structure of the E. coli disome - collided 70S ribosome | |||||||||
Map data | disome map after focused refinement on collided ribosome | |||||||||
Sample |
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Function / homology | Function and homology information RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation ...RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / 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 / translational termination / translation repressor activity / negative regulation of translational initiation / translational initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / response to reactive oxygen species / cytosolic ribosome assembly / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / single-stranded RNA binding / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.48 Å | |||||||||
Authors | Kratzat H / Buschauer R / Berninghausen O / Beckmann R | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nature / Year: 2022 Title: Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria. Authors: Kazuki Saito / Hanna Kratzat / Annabelle Campbell / Robert Buschauer / A Maxwell Burroughs / Otto Berninghausen / L Aravind / Rachel Green / Roland Beckmann / Allen R Buskirk / Abstract: Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled ...Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes. Here, using a genetic screen in Escherichia coli, we discovered a new rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNAs) to rescue upstream ribosomes. SmrB is recruited to ribosomes and is activated by collisions. Cryo-electron microscopy structures of collided disomes from E. coli and Bacillus subtilis show distinct and conserved arrangements of individual ribosomes and the composite SmrB-binding site. These findings reveal the underlying mechanisms by which ribosome collisions trigger ribosome rescue in bacteria. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13955.map.gz | 404.3 MB | EMDB map data format | |
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Header (meta data) | emd-13955-v30.xml emd-13955.xml | 69.2 KB 69.2 KB | Display Display | EMDB header |
Images | emd_13955.png | 81.9 KB | ||
Others | emd_13955_additional_1.map.gz emd_13955_additional_2.map.gz | 404.1 MB 23.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13955 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13955 | HTTPS FTP |
-Related structure data
Related structure data | 7qghMC 7qg8C 7qgnC 7qgrC 7qguC 7qh4C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13955.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | disome map after focused refinement on collided ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: disome map
File | emd_13955_additional_1.map | ||||||||||||
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Annotation | disome map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: local resolution filtered map
File | emd_13955_additional_2.map | ||||||||||||
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Annotation | local resolution filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : collided ribosome of the disome structure
+Supramolecule #1: collided ribosome of the disome structure
+Macromolecule #1: 5S rRNA
+Macromolecule #30: 23S rRNA
+Macromolecule #34: P-site tRNA
+Macromolecule #35: mRNA
+Macromolecule #36: 16S rRNA
+Macromolecule #58: A-site tRNA
+Macromolecule #2: 50S ribosomal protein L2
+Macromolecule #3: 50S ribosomal protein L3
+Macromolecule #4: 50S ribosomal protein L4
+Macromolecule #5: 50S ribosomal protein L5
+Macromolecule #6: 50S ribosomal protein L6
+Macromolecule #7: 50S ribosomal protein L11
+Macromolecule #8: 50S ribosomal protein L13
+Macromolecule #9: 50S ribosomal protein L14
+Macromolecule #10: 50S ribosomal protein L15
+Macromolecule #11: 50S ribosomal protein L16
+Macromolecule #12: 50S ribosomal protein L17
+Macromolecule #13: 50S ribosomal protein L18
+Macromolecule #14: 50S ribosomal protein L19
+Macromolecule #15: 50S ribosomal protein L20
+Macromolecule #16: 50S ribosomal protein L21
+Macromolecule #17: 50S ribosomal protein L22
+Macromolecule #18: 50S ribosomal protein L23
+Macromolecule #19: 50S ribosomal protein L24
+Macromolecule #20: 50S ribosomal protein L25
+Macromolecule #21: 50S ribosomal protein L27
+Macromolecule #22: 50S ribosomal protein L28
+Macromolecule #23: 50S ribosomal protein L29
+Macromolecule #24: 50S ribosomal protein L30
+Macromolecule #25: 50S ribosomal protein L32
+Macromolecule #26: 50S ribosomal protein L33
+Macromolecule #27: 50S ribosomal protein L34
+Macromolecule #28: 50S ribosomal protein L35
+Macromolecule #29: 50S ribosomal protein L36
+Macromolecule #31: 50S ribosomal protein L31
+Macromolecule #32: 50S ribosomal protein L1
+Macromolecule #33: 50S ribosomal protein L9
+Macromolecule #37: 30S ribosomal protein S2
+Macromolecule #38: 30S ribosomal protein S3
+Macromolecule #39: 30S ribosomal protein S4
+Macromolecule #40: 30S ribosomal protein S5
+Macromolecule #41: 30S ribosomal protein S6, non-modified isoform
+Macromolecule #42: 30S ribosomal protein S7
+Macromolecule #43: 30S ribosomal protein S8
+Macromolecule #44: 30S ribosomal protein S9
+Macromolecule #45: 30S ribosomal protein S10
+Macromolecule #46: 30S ribosomal protein S11
+Macromolecule #47: 30S ribosomal protein S12
+Macromolecule #48: 30S ribosomal protein S13
+Macromolecule #49: 30S ribosomal protein S14
+Macromolecule #50: 30S ribosomal protein S15
+Macromolecule #51: 30S ribosomal protein S16
+Macromolecule #52: 30S ribosomal protein S17
+Macromolecule #53: 30S ribosomal protein S18
+Macromolecule #54: 30S ribosomal protein S19
+Macromolecule #55: 30S ribosomal protein S20
+Macromolecule #56: 30S ribosomal protein S21
+Macromolecule #57: 30S ribosomal protein S1
+Macromolecule #59: MAGNESIUM ION
+Macromolecule #60: POTASSIUM ION
+Macromolecule #61: water
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75081 |