Structural analysis of uridine modifications in solved RNA structures

Naturally occurring uridine modifications in RNA play critical roles in modulating RNA stability, translation, and immune responses. While detection methods have advanced, a comprehensive structural analysis across experimentally determined RNA 3D structures remains limited. In this study, we systematically examined six uridine modifications-pseudouridine (PSU), 5-methyluridine (5MU), 3-methyluridine (UR3), O2'-methyluridine (OMU), 4-thiouridine (4SU), and 5,6-dihydrouridine (H2U)-using data from the Research Collaboratory for Structural Bioinformatics Protein Data Bank. After curation, we identified 2982 PSU, 736 5MU, 232 UR3, 429 OMU, 314 4SU, and 171 H2U residues across RNA-containing structures. These modifications were primarily found in ribosomal and transfer RNAs, often localized within hairpin secondary structures. Sugar pucker analysis revealed modification-specific preferences for C3'-<i>endo</i> and C2'-<i>endo</i> conformations. To assess structural impacts, we generated sequence-representative structures and compared modified versus unmodified forms using all-atom root-mean-square deviation analysis. Most modifications showed high similarity to their unmodified counterparts (RMSD [Formula: see text] 1.0 Å), though deviations were notable for certain PSU-, 5MU-, and 4SU-containing motifs. Despite overall similarity, interaction differences were observed between modified and canonical uridines. This work provides a detailed structural overview of uridine modifications, offering insights into their conformational behavior and implications for RNA function. These findings may inform future efforts in RNA-targeted therapeutics and structural biology.