High-resolution Analysis of Magnesium Ions in Ribosomes across Species and rRNA Modification States

With advances in structural biology, particularly cryogenic electron microscopy (cryo-EM), ribosome structures at increasingly high resolution have become available. These datasets enable detailed analysis of features that were previously inaccessible, such as ribosome-associated metal ions. Among these, Mg²⁺ plays a critical role in stabilizing the ribosome and supporting translation. In this study, we analyzed high-resolution structures of the large subunit from three organisms, including variants lacking specific rRNA chemical modifications. We found that Mg²⁺ distributions are largely conserved across species and modification states within highly conserved regions. However, we also observed differences in conserved but peripheral regions, as well as near 2′-O-methylation and pseudouridine sites upon loss of these modifications. In addition, we identified cases in which arginine or other positively charged residues of eukaryote-specific proteins in human ribosomes appear to substitute for Mg²⁺ ions present in bacterial ribosomes. Together, these findings are consistent with a well-conserved core and highlight a role for eukaryote-specific features in shaping Mg²⁺ distributions.