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| Title | Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis. |
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| Journal, issue, pages | Mol Cell, Vol. 86, Issue 10, Page 1896-11910.e7, Year 2026 |
| Publish date | May 21, 2026 |
 Authors | Qingrong Li / Gangshun Yi / Yue Wu / Sophy Xu / Jenny Chong / Xuhui Huang / Peijun Zhang / Dong Wang /   |
| PubMed Abstract | RNA polymerase II (RNA Pol II) is central to gene expression, but its catalytic mechanism remains elusive due to the absence of high-resolution structural data. The role of water molecules in RNA Pol ...RNA polymerase II (RNA Pol II) is central to gene expression, but its catalytic mechanism remains elusive due to the absence of high-resolution structural data. The role of water molecules in RNA Pol II catalysis is unknown. Here, we present 3 high-resolution cryo-electron microscopy structures of active Saccharomyces cerevisiae RNA Pol II elongation complexes in distinct catalytic states: two pre-catalysis states at 1.96 Å and 2.26 Å resolution and a post-catalysis state at 2.33 Å resolution. Each structure contains over 700-1,350 ordered water molecules, many located at functionally critical positions. Comparative analysis shows that these waters play essential roles in proton-transfer steps during RNA Pol II catalysis, facilitating substrate recognition and trigger-loop folding during nucleotide addition. Strikingly, these waters are conserved between prokaryotic and eukaryotic transcription machineries (see Mueller and Darst). These findings provide unprecedented mechanistic insights into RNA Pol II catalysis and reveal vital and evolutionarily conserved roles of water molecules in transcription. |
 External links | Mol Cell / PubMed:42066756 |
| Methods | EM (single particle) |
| Resolution | 2.33 - 3.12 Å |
| Structure data |  EMDB-53056: CryoEM structure of transcribing RNA polymerase II elongation complex_Local density map of RPB4/7  EMDB-53057: CryoEM structure of transcribing RNA polymerase II elongation complex_Composite map  EMDB-53060: CryoEM structure of transcribing RNA polymerase II elongation complex_Local density map of RPB9  EMDB-53062: CryoEM structure of transcribing RNA polymerase II elongation complex_Local density map of Jaw/RPB9  EMDB-53063: CryoEM structure of transcribing RNA polymerase II elongation complex_Local density map of RPB12/Wall  EMDB-53064: CryoEM structure of transcribing RNA polymerase II elongation complex_3D classification map containing the complete nucleic acid scaffold EMDB-54374, PDB-9ryb: |
| Chemicals |  ChemComp-MG:  ChemComp-ZN:  ChemComp-K:  ChemComp-DPO:  ChemComp-HOH: |
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 Keywords | TRANSCRIPTION / CryoEM / RNA Polymerase |
saccharomyces cerevisiae (brewer's yeast)