9SBO

Structure of Yeast RNA polymerase II elongation complex with ATP frame-4

Summary for 9SBO

• Entry DOI: 10.2210/pdb9sbo/pdb
• EMDB information: 54677 54733
• 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, ... (18 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: 563581.88

Authors

Yi, G.,Li, Q.,Zhang, P.,Wang, D. (deposition date: 2025-08-08, release date: 2026-07-01)

Primary citation

Yi, G.,Li, Q.,Holmberg, H.,Li, S.,Clare, D.K.,Wang, D.,Zhang, P.
Structural Dynamics of RNA Polymerase II During Nucleotide Addition Cycle.
Biorxiv, 2026

PubMed Abstract: RNA polymerase II (RNAPII) drives gene expression through iterative nucleotide addition cycles (NACs) comprising translocation, substrate binding, and catalysis. The lack of pre-catalysis and post-catalysis intermediates has precluded a complete mechanistic understanding of the NAC. Here we present 43 cryo-EM structures capturing distinct stages of the RNAPII elongation complex (EC) NAC, including previously intractable transition intermediates. We establish a continuous spectrum of RNAPII EC structural dynamics during the NAC, which can be divided into two coordinated phases: a substrate-induced EC tightening phase and a post-catalysis EC relaxation phase. For the substrate-induced EC tightening phase, the substrate binding initiates allosteric conformational changes across the entire RNAPII EC, including TL folding, funnel closure, clamp closure, transcription bubble ordering, and precise alignment of the RNA 3'-end with substrate to form a catalysis-competent configuration. For the post-catalysis EC relaxation phase, we captured the long-sought, short-lived post-catalysis product state and identified a series of intermediates that reveal a reverse conformational transition that facilitates rapid translocation. Together, our findings define a comprehensive structural and dynamic framework for RNAPII NAC, yielding a "molecular movie" of RNAPII in action and revealing a fundamental principle by which the enzyme balances speed and fidelity through coordinated conformational dynamics.

PubMed: 42282700
DOI: 10.64898/2026.06.04.730248

Experimental method

ELECTRON MICROSCOPY (3.97 Å)