9FP3

Ap4A bound in de novo transcription initiation T. thermophilus RNA polymerase complex with TC DNA template

9FP3 の概要

• エントリーDOI: 10.2210/pdb9fp3/pdb
• EMDBエントリー: 50634
• 分子名称: DNA-directed RNA polymerase subunit alpha, ZINC ION, PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER, ... (11 entities in total)
• 機能のキーワード: transcription-dna complex, non-canonical cap, transcription
• 由来する生物種: Thermus thermophilus HB8; 詳細
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 463961.36

構造登録者

Skerlova, J.,Dubankova, A.,Svachova, H.,Kouba, T. (登録日: 2024-06-12, 公開日: 2025-12-17, 最終更新日: 2026-01-21)

主引用文献

Serianni, V.M.,Skerlova, J.,Dubankova, A.K.,Skriba, A.,Svachova, H.,Vuckova, T.,Filimonenko, A.,Fabry, M.,Rezacova, P.,Kouba, T.,Cahova, H.
Molecular insight into 5' RNA capping with Np n Ns by bacterial RNA polymerase.
Nat.Chem.Biol., 2026

PubMed Abstract: RNA capped with dinucleoside polyphosphates has been discovered in bacteria and eukaryotes only recently. The likely mechanism of this specific capping involves direct incorporation of dinucleoside polyphosphates by RNA polymerase as noncanonical initiating nucleotides. However, how these compounds bind into the active site of RNA polymerase during transcription initiation is unknown. Here, we explored transcription initiation in vitro, using a series of DNA templates in combination with dinucleoside polyphosphates and model RNA polymerase from Thermus thermophilus. We observed that the transcription start site can vary on the basis of the compatibility of the specific template and dinucleoside polyphosphate. Cryo-electron microscopy structures of transcription initiation complexes with dinucleoside polyphosphates revealed that both nucleobase moieties can pair with the DNA template. The first encoded nucleotide pairs in a canonical Watson-Crick manner, whereas the second nucleobase pairs noncanonically in a reverse Watson-Crick manner. Our work provides a structural explanation of how dinucleoside polyphosphates initiate RNA transcription.

PubMed: 41513851
DOI: 10.1038/s41589-025-02134-5

実験手法

ELECTRON MICROSCOPY (2.42 Å)