+Open data
-Basic information
Entry | Database: PDB / ID: 6wnt | |||||||||||||||
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Title | 50S ribosomal subunit without free 5S rRNA and perturbed PTC | |||||||||||||||
Components |
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Keywords | RIBOSOME / 23S-cp5S rRNA / engineering | |||||||||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / negative regulation of translational initiation ...negative regulation of cytoplasmic translational initiation / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / negative regulation of translational initiation / translation repressor activity / translational initiation / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Loveland, A.B. / Korostelev, A.A. / Mankin, A.S. / Huang, S. / Aleksashin, N.A. / Klepacki, D. / Reier, K. / Kefi, A. / Szal, A. / Remme, J. ...Loveland, A.B. / Korostelev, A.A. / Mankin, A.S. / Huang, S. / Aleksashin, N.A. / Klepacki, D. / Reier, K. / Kefi, A. / Szal, A. / Remme, J. / Jaeger, L. / Vazquez-Laslop, N. | |||||||||||||||
Funding support | United States, Estonia, 4items
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Citation | Journal: Nat Commun / Year: 2020 Title: Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly. Authors: Shijie Huang / Nikolay A Aleksashin / Anna B Loveland / Dorota Klepacki / Kaspar Reier / Amira Kefi / Teresa Szal / Jaanus Remme / Luc Jaeger / Nora Vázquez-Laslop / Andrei A Korostelev / Alexander S Mankin / Abstract: 5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. ...5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. Here we used ribosome engineering to investigate whether 5S rRNA autonomy is critical for ribosome function and cell survival. By linking circularly permutated 5S rRNA with 23S rRNA we generated a bacterial strain devoid of free 5S rRNA. Viability of the engineered cells demonstrates that autonomous 5S rRNA is dispensable for cell growth under standard conditions and is unlikely to have essential functions outside the ribosome. The fully assembled ribosomes carrying 23S-5S rRNA are highly active in translation. However, the engineered cells accumulate aberrant 50S subunits unable to form stable 70S ribosomes. Cryo-EM analysis revealed a malformed peptidyl transferase center in the misassembled 50S subunits. Our results argue that the autonomy of 5S rRNA is preserved due to its role in ribosome biogenesis. | |||||||||||||||
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 | 6wnt.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6wnt.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 6wnt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/6wnt ftp://data.pdbj.org/pub/pdb/validation_reports/wn/6wnt | HTTPS FTP |
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-Related structure data
Related structure data | 21856MC 6wnvC 6wnwC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
+50S ribosomal protein ... , 30 types, 30 molecules bcdefghijklnopqrstuvwxyzABDEFa
-RNA chain , 1 types, 1 molecules 4
#31: RNA chain | Mass: 982729.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Engineered 23S rRNA with inserted circularly permuted 5S rRNA Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: Escherichia coli (E. coli) |
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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: 50S ribosomal subunit without free 5S rRNA and perturbed PTC Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 1.5 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS TALOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 489732 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21705 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||
NMR ensemble | Conformers submitted total number: 1 |