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.
Highlights
The ribosome performs the crucial task of translating the genetic code into proteins and varies in size from 2.3 MDa to over 4 MDa across the three domains of life (Melnikov et al, 2012)
We determined the structure of the Escherichia coli 70S ribosome in the classical state with messenger RNA (mRNA) and transfer RNAs (tRNAs) bound in the Aminoacyl-tRNA and Peptidyl-tRNA sites (A site and P site, respectively)
Partial density for Exit-site (E-site) tRNA is visible in the maps, for the 3’-terminal C75 and A76 nucleotides
Summary
The ribosome performs the crucial task of translating the genetic code into proteins and varies in size from 2.3 MDa to over 4 MDa across the three domains of life (Melnikov et al, 2012). To carry out the highly coordinated process of translation, the ribosome orchestrates the binding and readout of messenger RNA (mRNA) and transfer RNAs (tRNAs), coupled with a multitude of interactions between the small and large ribosomal subunits and a host of translation factors. These molecular interactions are accompanied by a wide range of conformational dynamics that contribute to translation accuracy and speed. Development of small molecule drugs such as antibiotics is hampered at the typical resolution of available X-ray crystal structures of the ribosome (~3 Å) (Arenz and Wilson, 2016; Yusupova and Yusupov, 2017). Understanding of the molecular interactions in the ribosome in chemical detail would provide a foundation for biochemical and biophysical approaches that probe ribosome function and aid antibiotic discovery
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