9CBX

Tetrahymena ribozyme with automatically identified water and magnesium ions

9CBX の概要

• エントリーDOI: 10.2210/pdb9cbx/pdb
• EMDBエントリー: 42499
• 分子名称: RNA (387-MER), MAGNESIUM ION (3 entities in total)
• 機能のキーワード: ribozyme, magnesium ions, water, rna
• 由来する生物種: Tetrahymena thermophila
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 126506.46

構造登録者

Kretsch, R.C.,Li, S.,Pintilie, G.,Palo, M.Z.,Case, D.A.,Das, R.,Zhang, K.,Chiu, W. (登録日: 2024-06-20, 公開日: 2024-11-20, 最終更新日: 2025-06-18)

主引用文献

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. Here we investigated water through cryogenic electron microscopy (cryo-EM) on a highly solvated molecule: the Tetrahymena ribozyme. By using segmentation-guided water and ion modelling (SWIM), an approach combining resolvability and chemical parameters, we automatically modelled 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, supporting their assignment as water and suggesting a biophysical explanation for their elusiveness to conventional atomic coordinate modelling. 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 molecular dynamics simulations.

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

実験手法

ELECTRON MICROSCOPY (2.2 Å)