Nature Communications (May 2025)

Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations

  • Elisa Posani,
  • Pavel Janoš,
  • Daniel Haack,
  • Navtej Toor,
  • Massimiliano Bonomi,
  • Alessandra Magistrato,
  • Giovanni Bussi

DOI
https://doi.org/10.1038/s41467-025-59769-0
Journal volume & issue
Vol. 16, no. 1
pp. 1 – 11

Abstract

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Abstract 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 matches experimental data, and we reveal inaccuracies of single-structure approaches in modeling flexible regions. An analysis of all RNA-containing structures deposited in the Protein Data Bank reveals 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.