SNAP output for PDB entry 7r4x [SNAP web server]

PDB-id

7r4x; SNAP-derived features in text and JSON formats; DNAproDB

Class

ribosome

Method

cryo-EM (2.15 Å)

Summary

cryo-EM reconstruction of the human 40s ribosomal subunit - full map

Reference

Pellegrino S, Dent KC, Spikes T, Warren AJ (2023): "Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 angstrom resolution." Nucleic Acids Res., 51, 4043-4054. doi: 10.1093/nar/gkad194.

Abstract

The chemical modification of ribosomal RNA and proteins is critical for ribosome assembly, for protein synthesis and may drive ribosome specialisation in development and disease. However, the inability to accurately visualise these modifications has limited mechanistic understanding of the role of these modifications in ribosome function. Here we report the 2.15 Å resolution cryo-EM reconstruction of the human 40S ribosomal subunit. We directly visualise post-transcriptional modifications within the 18S rRNA and four post-translational modifications of ribosomal proteins. Additionally, we interpret the solvation shells in the core regions of the 40S ribosomal subunit and reveal how potassium and magnesium ions establish both universally conserved and eukaryote-specific coordination to promote the stabilisation and folding of key ribosomal elements. This work provides unprecedented structural details for the human 40S ribosomal subunit that will serve as an important reference for unravelling the functional role of ribosomal RNA modifications.