+Open data
-Basic information
Entry | Database: PDB / ID: 7qgh | ||||||
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Title | Structure of the E. coli disome - collided 70S ribosome | ||||||
Components |
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Keywords | RIBOSOME / Ribosome rescue / disome / ribosome collision / stalling / no-go complex | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.48 Å | ||||||
Authors | Kratzat, H. / Buschauer, R. / Berninghausen, O. / Beckmann, R. | ||||||
Funding support | Germany, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7qgh.cif.gz | 3.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7qgh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/7qgh ftp://data.pdbj.org/pub/pdb/validation_reports/qg/7qgh | HTTPS FTP |
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-Related structure data
Related structure data | 13955MC 7qg8C 7qgnC 7qgrC 7qguC 7qh4C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 6 types, 6 molecules ONMx0u
#1: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 1845258627 |
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#30: RNA chain | Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) |
#34: RNA chain | Mass: 24060.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 1847035720 |
#35: RNA chain | Mass: 221443.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) |
#36: RNA chain | Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 1758835854 |
#58: RNA chain | Mass: 23545.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 1851743410 |
+50S ribosomal protein ... , 31 types, 31 molecules PQRSTVWXYZabcdefghijklmnopqrLCU
+30S ribosomal protein ... , 21 types, 21 molecules 123456789ABDEFGHIJKst
-Non-polymers , 3 types, 12 molecules
#59: Chemical | #60: Chemical | ChemComp-K / | #61: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: collided ribosome of the disome structure / Type: RIBOSOME / Entity ID: #1-#58 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75081 / Symmetry type: POINT |