Structure of the bacterial ribosome at 2 Å resolution

Abstract
Data availability
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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

1. Watson ZL
2. Ward FR
3. Meheust R
4. Ad O
5. Schepartz A
6. Banfield JF
7. Cate JHD
(2020) Ribosome coordinates
Protein Data Bank, 7K00.

http://www.rcsb.org/structure/7K00
1. Watson ZL
2. Ward FR
3. Meheust R
4. Ad O
5. Schepartz A
6. Banfield JF
7. Cate JHD
(2020) 70S ribosome composite map
Electron Microsopy Databank, EMD-22586.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-22586
1. Watson ZL
2. Ward FR
3. Meheust R
4. Ad O
5. Schepartz A
6. Banfield JF
7. Cate JHD
(2020) 70S ribosome
Electron Microsopy Databank, EMD-22607.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-22607
1. Watson ZL
2. Ward FR
3. Meheust R
4. Ad O
5. Schepartz A
6. Banfield JF
7. Cate JHD
(2020) 50S subunit
Electron Microsopy Databank, EMD-22614.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-22614
1. Watson ZL
2. Ward FR
3. Meheust R
4. Ad O
5. Schepartz A
6. Banfield JF
7. Cate JHD
(2020) 30S subunit
Electron Microsopy Databank, EMD-22632.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-22632
1. Watson ZL
2. Ward FR
3. Meheust R
4. Ad O
5. Schepartz A
6. Banfield JF
7. Cate JHD
(2020) 30S subunit head
Electron Microsopy Databank, EMD-22635.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-22635
1. Watson ZL
2. Ward FR
3. Meheust R
4. Ad O
5. Schepartz A
6. Banfield JF
7. Cate JHD
(2020) 30S subunit platform
Electron Microsopy Databank, EMD-22636.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-22636
1. Watson ZL
2. Ward FR
3. Meheust R
4. Ad O
5. Schepartz A
6. Banfield JF
7. Cate JHD
(2020) 50S subunit CP maps
Electron Microsopy Databank, EMD-22637.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-22637
1. Watson ZL
2. Ward FR
3. Meheust R
4. Ad O
5. Schepartz A
6. Banfield JF
7. Cate JHD
(2020) Raw movies
EMPIAR, 10509.

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10509/

The following previously published data sets were used

1. Smith LM
(2017) E. coli Proteoform Families and G-PTM-D Database Expansion
MassIVE, accession MSV000081144.

https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp

Article and author information

Author details

Zoe L Watson

Chemistry, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4877-7914
Fred R Ward

Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3825-5095
Raphaël Méheust

Earth and Planetary Science, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.
Omer Ad

Chemistry, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.
Alanna Schepartz

Chemistry, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-2127-3932
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.
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.

"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.

Copyright

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.