SNAP output for PDB entry 6wub [SNAP web server]

PDB-id

6wub; SNAP-derived features in text and JSON formats; DNAproDB

Class

ribosome

Method

cryo-EM (3.2 Å)

Summary

30s subunit (head) of 70s ribosome enterococcus faecalis multibody refinement

Reference

Murphy EL, Singh KV, Avila B, Kleffmann T, Gregory ST, Murray BE, Krause KL, Khayat R, Jogl G (2020): "Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis." Sci Rep, 10, 16301. doi: 10.1038/s41598-020-73199-6.

Abstract

Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen.