9Q87

Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+

This is a non-PDB format compatible entry.

Summary for 9Q87

• Entry DOI: 10.2210/pdb9q87/pdb
• EMDB information: 15793
• Descriptor: 30S, Small ribosomal subunit protein uS10, Small ribosomal subunit protein uS11, ... (61 entities in total)
• Functional Keywords: ribosome, magnesium, mg2+, potassium, k+
• Biological source: Escherichia coli B; More
• Total number of polymer chains: 55
• Total formula weight: 2198636.06

Authors

Leonarski, F.,Henning-Knechtel, A.,Kirmizialtin, S.,Ennifar, E.,Auffinger, P. (deposition date: 2025-02-23, release date: 2025-05-14, Last modification date: 2025-11-19)

Primary citation

Leonarski, F.,Henning-Knechtel, A.,Kirmizialtin, S.,Ennifar, E.,Auffinger, P.
Principles of ion binding to RNA inferred from the analysis of a 1.55 angstrom resolution bacterial ribosome structure - Part I: Mg2.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: The importance of Mg2+ ions for RNA structure and function cannot be overstated. Several attempts were made to establish a comprehensive Mg2+ binding site classification. However, such descriptions were hampered by poorly modelled ion binding sites as observed in a recent cryo-EM 1.55 Å Escherichia coli ribosome structure where incomplete ion assignments blurred our understanding of their binding patterns. We revisited this model to establish general binding principles applicable to any RNA of sufficient resolution. These principles rely on the 2.9 Å distance separating two water molecules bound in cis to Mg2+. By applying these rules, we could assign all Mg2+ ions bound with 2-4 non-water oxygens. We also uncovered unanticipated motifs where up to five adjacent nucleotides wrap around a single ion. The formation of such motifs involves a hierarchical Mg2+ ion dehydration process that plays a significant role in ribosome biogenesis and in the folding of large RNAs. Besides, we established a classification of the Mg2+…Mg2+ and Mg2+…K+ ion pairs observed in this ribosome. Overall, the uncovered binding principles enhance our understanding of the roles of ions in RNA structure and will help refining the solvation shell of other RNA systems.

PubMed: 39791453
DOI: 10.1093/nar/gkae1148

Experimental method

ELECTRON MICROSCOPY (1.55 Å)