9GDA

RNAP-TopoI complex on duplex scaffold

9GDA の概要

• エントリーDOI: 10.2210/pdb9gda/pdb
• EMDBエントリー: 51259
• 分子名称: DNA-directed RNA polymerase subunit alpha, ZINC ION, DNA-directed RNA polymerase subunit beta, ... (10 entities in total)
• 機能のキーワード: rna polymerase, topoisomerase, dna topology, transcription
• 由来する生物種: Escherichia coli; 詳細
• タンパク質・核酸の鎖数: 9
• 化学式量合計: 520031.48

構造登録者

Vidmar, V.,Weixlbaumer, A.,Lamour, V. (登録日: 2024-08-05, 公開日: 2025-11-05, 最終更新日: 2026-01-28)

主引用文献

Vidmar, V.,Borde, C.,Bruno, L.,Miropolskaya, N.,Takacs, M.,Batisse, C.,Saint-Andre, C.,Zhu, C.,Espeli, O.,Lamour, V.,Weixlbaumer, A.
DNA topoisomerase I acts as supercoiling sensor for bacterial transcription elongation.
Nat.Struct.Mol.Biol., 33:134-144, 2026

PubMed Abstract: During transcription, RNA polymerase (RNAP) continuously unwinds and rewinds DNA, generating negative and positive supercoils upstream and downstream, respectively. Using single-particle cryo-EM, we elucidated how bacterial RNAP and DNA topoisomerase I (TopoI), which relaxes negative supercoils, operate in close spatial proximity. TopoI binds to relaxed DNA upstream of RNAP, and this involves a conformational switch in the TopoI functional domains. This suggests that TopoI exerts a sensing role before the formation of negative supercoils. On DNA substrates mimicking negatively supercoiled DNA, TopoI threads one strand into the active site for cleavage and binds the complementary strand with an auxiliary domain. Transcriptomic and phenotypic analyses suggest that mutations affecting conformational changes in TopoI impact gene expression and operon polarity in bacteria. In summary, we propose a comprehensive model for DNA relaxation in the proximity of active bacterial transcription.

PubMed: 41326756
DOI: 10.1038/s41594-025-01703-5

実験手法

ELECTRON MICROSCOPY (2.7 Å)