8TOE

Escherichia coli RNA polymerase unwinding intermediate (I1c) at the lambda PR promoter

8TOE の概要

• エントリーDOI: 10.2210/pdb8toe/pdb
• EMDBエントリー: 41448
• 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: dna-dependent rna polymerase, transcription, intermediate, dna promoter, dna unwinding, transcription-dna complex, transcription/dna
• 由来する生物種: Escherichia coli (strain K12); 詳細
• タンパク質・核酸の鎖数: 9
• 化学式量合計: 563300.71

構造登録者

Darst, S.A.,Saecker, R.M.,Mueller, A.U. (登録日: 2023-08-03, 公開日: 2024-07-03, 最終更新日: 2025-06-04)

主引用文献

Saecker, R.M.,Mueller, A.U.,Malone, B.,Chen, J.,Budell, W.C.,Dandey, V.P.,Maruthi, K.,Mendez, J.H.,Molina, N.,Eng, E.T.,Yen, L.Y.,Potter, C.S.,Carragher, B.,Darst, S.A.
Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.
Nat.Struct.Mol.Biol., 31:1778-1788, 2024

PubMed Abstract: During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAPs), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, here we use time-resolved cryogenic electron microscopy (cryo-EM) to capture four intermediates populated 120 ms or 500 ms after mixing Escherichia coli σ-RNAP and the λP promoter. Cryo-EM snapshots revealed that the upstream edge of the transcription bubble unpairs rapidly, followed by stepwise insertion of two conserved nontemplate strand (nt-strand) bases into RNAP pockets. As the nt-strand 'read-out' extends, the RNAP clamp closes, expelling an inhibitory σ domain from the active-site cleft. The template strand is fully unpaired by 120 ms but remains dynamic, indicating that yet unknown conformational changes complete RPo formation in subsequent steps. Given that these events likely describe DNA opening at many bacterial promoters, this study provides insights into how DNA sequence regulates steps of RPo formation.

PubMed: 38951624
DOI: 10.1038/s41594-024-01349-9

実験手法

ELECTRON MICROSCOPY (2.9 Å)