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- EMDB-13952: Structure of the collided E. coli disome - VemP-stalled 70S ribosome -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13952 | |||||||||
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Title | Structure of the collided E. coli disome - VemP-stalled 70S ribosome | |||||||||
![]() | disome map after focused refinement on stalled ribosome | |||||||||
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Function / homology | ![]() 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 / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.97 Å | |||||||||
![]() | Kratzat H / Buschauer R / Berninghausen O / Beckmann R | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 406.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 69.8 KB 69.8 KB | Display Display | ![]() |
Images | ![]() | 59 KB | ||
Others | ![]() ![]() | 21.2 MB 404.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qg8MC ![]() 7qghC ![]() 7qgnC ![]() 7qgrC ![]() 7qguC ![]() 7qh4C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | disome map after focused refinement on stalled ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: local resolution filtered map
File | emd_13952_additional_1.map | ||||||||||||
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Annotation | local resolution filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: disome map
File | emd_13952_additional_2.map | ||||||||||||
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Annotation | disome map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : stalled/leading ribosome of the collided disome structure
+Supramolecule #1: stalled/leading ribosome of the collided disome structure
+Macromolecule #1: A-site tRNA
+Macromolecule #3: P-site tRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #34: 23S rRNA
+Macromolecule #37: 16S rRNA
+Macromolecule #2: VemP nascent chain
+Macromolecule #5: 50S ribosomal protein L2
+Macromolecule #6: 50S ribosomal protein L3
+Macromolecule #7: 50S ribosomal protein L4
+Macromolecule #8: 50S ribosomal protein L5
+Macromolecule #9: 50S ribosomal protein L6
+Macromolecule #10: 50S ribosomal protein L9
+Macromolecule #11: 50S ribosomal protein L11
+Macromolecule #12: 50S ribosomal protein L13
+Macromolecule #13: 50S ribosomal protein L14
+Macromolecule #14: 50S ribosomal protein L15
+Macromolecule #15: 50S ribosomal protein L16
+Macromolecule #16: 50S ribosomal protein L17
+Macromolecule #17: 50S ribosomal protein L18
+Macromolecule #18: 50S ribosomal protein L19
+Macromolecule #19: 50S ribosomal protein L20
+Macromolecule #20: 50S ribosomal protein L21
+Macromolecule #21: 50S ribosomal protein L22
+Macromolecule #22: 50S ribosomal protein L23
+Macromolecule #23: 50S ribosomal protein L24
+Macromolecule #24: 50S ribosomal protein L25
+Macromolecule #25: 50S ribosomal protein L27
+Macromolecule #26: 50S ribosomal protein L28
+Macromolecule #27: 50S ribosomal protein L29
+Macromolecule #28: 50S ribosomal protein L30
+Macromolecule #29: 50S ribosomal protein L32
+Macromolecule #30: 50S ribosomal protein L33
+Macromolecule #31: 50S ribosomal protein L34
+Macromolecule #32: 50S ribosomal protein L35
+Macromolecule #33: 50S ribosomal protein L36
+Macromolecule #35: 50S ribosomal protein L31
+Macromolecule #36: 50S ribosomal protein L1
+Macromolecule #38: 30S ribosomal protein S2
+Macromolecule #39: 30S ribosomal protein S3
+Macromolecule #40: 30S ribosomal protein S4
+Macromolecule #41: 30S ribosomal protein S5
+Macromolecule #42: 30S ribosomal protein S6, non-modified isoform
+Macromolecule #43: 30S ribosomal protein S7
+Macromolecule #44: 30S ribosomal protein S8
+Macromolecule #45: 30S ribosomal protein S9
+Macromolecule #46: 30S ribosomal protein S10
+Macromolecule #47: 30S ribosomal protein S11
+Macromolecule #48: 30S ribosomal protein S12
+Macromolecule #49: 30S ribosomal protein S13
+Macromolecule #50: 30S ribosomal protein S14
+Macromolecule #51: 30S ribosomal protein S15
+Macromolecule #52: 30S ribosomal protein S16
+Macromolecule #53: 30S ribosomal protein S17
+Macromolecule #54: 30S ribosomal protein S18
+Macromolecule #55: 30S ribosomal protein S19
+Macromolecule #56: 30S ribosomal protein S20
+Macromolecule #57: 30S ribosomal protein S21
+Macromolecule #58: MAGNESIUM ION
+Macromolecule #59: POTASSIUM ION
+Macromolecule #60: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75081 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |