Structure of the bacterial ribosome at 2 Å resolution
- University of California, Berkeley, United States
Abstract
Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analysis of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.
Data availability
Ribosome coordinates have been deposited in the Protein Data Bank (entry 7K00), maps in the EM Database (entries EMD-22586, EMD-22607, EMD-22614, EMD-22632, EMD-22635, EMD-22636, and EMD-22637 for the 70S ribosome composite map, 70S ribosome, 50S subunit, 30S subunit, 30S subunit head, 30S subunit platform, and 50S subunit CP maps, respectively), and raw movies in EMPIAR (entry EMPIAR-10509).
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70S ribosome composite mapElectron Microsopy Databank, EMD-22586.
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30S subunit headElectron Microsopy Databank, EMD-22635.
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30S subunit platformElectron Microsopy Databank, EMD-22636.
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50S subunit CP mapsElectron Microsopy Databank, EMD-22637.
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E. coli Proteoform Families and G-PTM-D Database ExpansionMassIVE, accession MSV000081144.
Article and author information
Author details
Funding
National Science Foundation
- Zoe L Watson
- Omer Ad
- Alanna Schepartz
- Jamie HD Cate
National Institutes of Health
- Fred R Ward
Innovative Genomics Institute
- Raphaël Méheust
- Jillian F Banfield
Chan Zuckerberg Biohub
- Raphaël Méheust
- Jillian F Banfield
Agilent Technologies
- Omer Ad
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2020, Watson et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Structure of the bacterial ribosome at 2 Å resolution
eLife 9:e60482.
https://doi.org/10.7554/eLife.60482
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