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TitleComplex water networks visualized by cryogenic electron microscopy of RNA.
Journal, issue, pagesNature, Vol. 642, Issue 8066, Page 250-259, Year 2025
Publish dateMar 11, 2025
AuthorsRachael C Kretsch / Shanshan Li / Grigore Pintilie / Michael Z Palo / David A Case / Rhiju Das / Kaiming Zhang / Wah Chiu /
PubMed AbstractThe 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 ...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.
External linksNature / PubMed:40068818 / PubMed Central
MethodsEM (single particle)
Resolution2.2 - 2.31 Å
Structure data

42498

9cbw

9cby

EMDB-42498: Tetrahymena ribozyme with water and magnesium ions
PDB-9cbw: Tetrahymena ribozyme with consensus water and magnesium ions
PDB-9cby: Tetrahymena ribozyme with automatically identified water and magnesium ions
Method: EM (single particle) / Resolution: 2.31 Å

42499

9cbu

9cbx

EMDB-42499: Tetrahymena ribozyme with water and magnesium ions
PDB-9cbu: Tetrahymena ribozyme with consensus water and magnesium ions
PDB-9cbx: Tetrahymena ribozyme with automatically identified water and magnesium ions
Method: EM (single particle) / Resolution: 2.2 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

Source
  • tetrahymena thermophila (eukaryote)
KeywordsRNA / Ribozyme / Magnesium ions / Water

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