Structure of the bacterial ribosome at 2 Å resolution
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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 analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.
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In the E. coli 70S ribosome, 309 Mg2+ and 2 Zn2+ ions were assigned by cryo-EM, but K+ was not included in the solvent and was not assigned.
“In the E. coli 70S ribosome, 309 Mg2+ and 2 Zn2+ ions were assigned by this method, but K+ was not included in the solvent and was not assigned.67”
From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [67]
Two complexes, Rpl12B-Rmt2 and Rpl7A-Fpr4, involving enzymes that introduce protein modifications such as arginine methylations or proline isomerizations, provide insight into mechanisms that expand the chemical diversity of ribosomal proteins at functional sites and possibly regulate translation.
“Two complexes, Rpl12B–Rmt2 and Rpl7A–Fpr4, involving enzymes that introduce protein modifications such as arginine methylations or proline isomerizations (47), provide insight into mechanisms that expand the chemical diversity of ribosomal proteins at functional sites (48) and possibly regulate translation (49).”
From Computed structures of core eukaryotic protein complexes (2021) · cites this paper as [48]
Ribosome structures can now be determined to better than 2 Å resolution using cryo-electron microscopy (cryo-EM).
“Ribosome structures can now be determined to better than 2 Å resolution using cryo-electron microscopy (cryo-EM).67”
From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [67]
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Flagged first, then by citations
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- Authors
- Watson, Z. L., Ward, F. R., Méheust, R., Ad, O., Schepartz, A., Banfield, J. F., & Cate, J. H.
- Affiliations
- University of California, Berkeley (US)
- Innovative Genomics Institute (US)
- Yale University (US)
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Cate, Jamie HD
- ORCID
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2020-09-14
- Volume
- 9
- ISSN
- 2050-084X (ISSN-L)
- OpenAlex
- W4211030178
- Cited by
- 263
- References
- 130
- Citations by year
- 2026: 38 · 2025: 33 · 2024: 53 · 2023: 50 · 2022: 50 · 2021: 32 · 2020: 5
- FWCI
- 11.14
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- HAL (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- Funders
- National Science Foundation (CHE-2021739)
- National Institutes of Health (R01-114454)
- Innovative Genomics Institute
- Chan Zuckerberg Biohub
- Agilent Technologies
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- bacterial ribosome, ribosome structure, ribosomal proteins, isopeptide bonds, tRNA binding sites, paromomycin, ribosome evolution, translation (biology)
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