Structure of the bacterial ribosome at 2 Å resolution

  1. Zoe L Watson
  2. Fred R Ward
  3. Raphaël Méheust
  4. Omer Ad
  5. Alanna Schepartz
  6. Jillian F Banfield
  7. Jamie HD Cate  Is a corresponding author
  1. 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).

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Zoe L Watson

    Chemistry, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4877-7914
  2. Fred R Ward

    Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3825-5095
  3. Raphaël Méheust

    Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Omer Ad

    Chemistry, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Alanna Schepartz

    Chemistry, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2127-3932
  6. Jillian F Banfield

    Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Jamie HD Cate

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
    For correspondence
    j-h-doudna-cate@berkeley.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5965-7902

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.

Reviewing Editor

  1. Sjors HW Scheres, MRC Laboratory of Molecular Biology, United Kingdom

Publication history

  1. Received: June 27, 2020
  2. Accepted: September 11, 2020
  3. Accepted Manuscript published: September 14, 2020 (version 1)
  4. Version of Record published: October 12, 2020 (version 2)

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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  1. Zoe L Watson
  2. Fred R Ward
  3. Raphaël Méheust
  4. Omer Ad
  5. Alanna Schepartz
  6. Jillian F Banfield
  7. Jamie HD Cate
(2020)
Structure of the bacterial ribosome at 2 Å resolution
eLife 9:e60482.
https://doi.org/10.7554/eLife.60482

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