PT - JOURNAL ARTICLE AU - Posani, Elisa AU - Janoš, Pavel AU - Haack, Daniel AU - Toor, Navtej AU - Bonomi, Massimiliano AU - Magistrato, Alessandra AU - Bussi, Giovanni TI - Ensemble Refinement of mismodeled cryo-EM RNA Structures Using All-Atom Simulations AID - 10.1101/2024.07.24.604258 DP - 2024 Jan 01 TA - bioRxiv PG - 2024.07.24.604258 4099 - http://biorxiv.org/content/early/2024/09/18/2024.07.24.604258.short 4100 - http://biorxiv.org/content/early/2024/09/18/2024.07.24.604258.full AB - The advent of single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution imaging of large macromolecules, enhancing functional insights. However, current cryo-EM refinement tools condense all single-particle images into a single structure, which can misrepresent highly flexible molecules like RNAs. Here, we combine molecular dynamics simulations with cryo-EM density maps to better account for the structural dynamics of a complex and biologically relevant RNA macromolecule. Namely, using metainference, a Bayesian method, we reconstruct an ensemble of structures of the group II intron ribozyme, which better match experimental data, and we reveal inaccuracies of single-structure approaches in modeling flexible regions. An analysis of all RNA-containing structures deposited in the PDB reveal that this issue affects most cryo-EM structures in the 2.5—4 Å range. Thus, RNA structures determined by cryo-EM require careful handling, and our method may be broadly applicable to other RNA systems.Competing Interest StatementThe authors have declared no competing interest.