Complex water networks visualized by cryogenic electron microscopy of RNA
The stability and function of biomolecules are directly influenced by their myriad interactions with water1–16. In this study, we investigated water through cryogenic electron microscopy (cryo-EM) on a highly solvated molecule, the Tetrahymena ribozyme, determined at 2.2 and 2.3 Å resolutions. By employing segmentation-guided water and ion modeling (SWIM)17,18, an approach combining resolvability and chemical parameters, we automatically modeled and cross-validated water molecules and Mg2+ ions in the ribozyme core, revealing the extensive involvement of water in mediating RNA non-canonical interactions. Unexpectedly, in regions where SWIM does not model ordered water, we observed highly similar densities in both cryo-EM maps. In many of these regions, the cryo-EM densities superimpose with complex water networks predicted by molecular dynamics (MD), supporting their assignment as water and suggesting a biophysical explanation for their elusiveness to conventional atomic coordinate modeling. Our study demonstrates an approach to unveil both rigid and flexible waters that surround biomolecules through cryo-EM map densities, statistical and chemical metrics, and MD simulations.Abstract
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Supplementary Video 1
Animation of Tetrahymena ribozyme cryo-EM map at 2.2 Å resolution, with modeled RNA, ions, and water molecules. Zoom-in sequences illustrate panels C, H, E, and F from Fig. 3.
Supplementary Video 2
Animation of Tetrahymena ribozyme cryo-EM maps at 2.2 and 2.3 Å resolution, with modeled RNA, ions, and water molecules. Maps are displayed at 3σ above background. Illustrates the 3-dimensional context for Fig. 5B-E.
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Kretsch, R.C., Li, S., Pintilie, G. et al. Complex water networks visualized by cryogenic electron microscopy of RNA. Nature (2025). https://doi.org/10.1038/s41586-025-08855-w
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DOI: https://doi.org/10.1038/s41586-025-08855-w
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