Sub-2 Å Cryo-EM Structures of Transcribing RNA Polymerase II Reveal Critical Roles of Water Molecules in Catalysis

Published: 29 April 2026| Version 1 | DOI: 10.17632/6trdb8j5ty.1
Contributors:
Qingrong Li,
,
,

Description

This dataset contains three high-resolution cryo-EM structures of the RNA polymerase II elongation complexes associated with our Molecular Cell study (Title: Sub-2 Å Cryo-EM Structures of Transcribing RNA Polymerase II Reveal Critical Roles of Water Molecules in Catalysis). The structures correspond to two pre-catalysis states (with and without Elf1) and one post-catalysis state (PDB IDs: 9SV6, 9QEB, 9RYB). In the PDB-deposited structures, water molecules are assigned and renumbered according to standard annotation procedures. The models provided here retain the author originally-defined water chain and numbering used throughout the manuscript.

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The structures were determined using high-resolution cryo-electron microscopy of Saccharomyces cerevisiae RNA polymerase II elongation complexes assembled in vitro. Pre-catalysis and post-catalysis states were generated by controlling nucleotide incorporation conditions, followed by cryo-EM data collection and 3D reconstruction using standard single-particle analysis workflows. Atomic models were built and refined against cryo-EM density maps using established procedures. Water molecules were identified based on density thresholds, Q-score validation, and coordination geometry analysis. The models provided in this dataset correspond to the author originally-defined water chain and numbering used in the manuscript. Detailed experimental procedures, data processing, and validation methods are described in the associated Molecular Cell publication (Title: Sub-2 Å Cryo-EM Structures of Transcribing RNA Polymerase II Reveal Critical Roles of Water Molecules in Catalysis).

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Protein Structure

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