9RYB

CryoEM structure of transcribing RNA polymerase II elongation complex in post-catalysis state

Summary for 9RYB

• Entry DOI: 10.2210/pdb9ryb/pdb
• EMDB information: 54374
• Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, ... (20 entities in total)
• Functional Keywords: cryoem, rna polymerase, transcription
• Biological source: Saccharomyces cerevisiae (brewer's yeast); More
• Total number of polymer chains: 15
• Total formula weight: 566636.76

Authors

Li, Q.,Yi, G.,Zhang, P.,Wang, D. (deposition date: 2025-07-15, release date: 2026-05-27)

Primary citation

Li, Q.,Yi, G.,Wu, Y.,Xu, S.,Chong, J.,Huang, X.,Zhang, P.,Wang, D.
Sub-2 angstrom cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis.
Mol.Cell, 2026

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 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.

PubMed: 42066756
DOI: 10.1016/j.molcel.2026.04.007

Experimental method

ELECTRON MICROSCOPY (2.33 Å)