9CBX

Tetrahymena ribozyme with automatically identified water and magnesium ions

Summary for 9CBX

• Entry DOI: 10.2210/pdb9cbx/pdb
• EMDB information: 42499
• Descriptor: RNA (387-MER), MAGNESIUM ION (3 entities in total)
• Functional Keywords: ribozyme, magnesium ions, water, rna
• Biological source: Tetrahymena thermophila
• Total number of polymer chains: 1
• Total formula weight: 126506.46

Authors

Kretsch, R.C.,Li, S.,Pintilie, G.,Palo, M.Z.,Case, D.A.,Das, R.,Zhang, K.,Chiu, W. (deposition date: 2024-06-20, release date: 2024-11-20, Last modification date: 2025-06-18)

Primary citation

Kretsch, R.C.,Li, S.,Pintilie, G.,Palo, M.Z.,Case, D.A.,Das, R.,Zhang, K.,Chiu, W.
Complex water networks visualized by cryogenic electron microscopy of RNA.
Nature, 642:250-259, 2025

PubMed Abstract: The stability and function of biomolecules are directly influenced by their myriad interactions with water. 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), an approach combining resolvability and chemical parameters, we automatically modeled and cross-validated water molecules and Mg 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.

PubMed: 40068818
DOI: 10.1038/s41586-025-08855-w

Experimental method

ELECTRON MICROSCOPY (2.2 Å)