10MG

CBR9379 bound Open2 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL)

10MG の概要

• エントリーDOI: 10.2210/pdb10mg/pdb
• EMDBエントリー: 75285
• 分子名称: template DNA, ZINC ION, 3-{[(2,6-dichlorophenyl)carbamoyl]amino}-N-hydroxy-N'-phenyl-5-(trifluoromethyl)benzenecarboximidamide, ... (12 entities in total)
• 機能のキーワード: transcription, rna polymerase, dna/rna, nucleotide addition cycle
• 由来する生物種: Escherichia coli; 詳細
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 416460.05

構造登録者

Dhingra, Y.,Darst, S.A. (登録日: 2026-01-27, 公開日: 2026-06-24)

主引用文献

Dhingra, Y.,Landick, R.,Campbell, E.A.,Darst, S.A.
RNA polymerase inhibitors reveal active-site motions essential for the nucleotide-addition cycle.
Biorxiv, 2026

PubMed Abstract: The nucleotide-addition cycle (NAC) of multi-subunit DNA-dependent RNA polymerases (RNAPs) involves coordinated conformational changes in conserved active-site structural elements, including the trigger loop (TL). The TL is open (unfolded) in most RNAP structures but can close (fold) in substrate-bound (post- or pre-translocated) states of the RNAP, promoting catalysis. TL closure has been associated with closure of another conserved structural element, the Rim-Helices/F-loop (RH-FL), but the role of the RH-FL in the NAC is unclear. Antibiotic leads CBR9379 and AAP-SO inhibit the and RNAPs, respectively, by binding in a pocket formed by the bridge helix and RH-FL. The precise mechanism of action for these inhibitors is yet to be defined. We present cryo-electron microscopy structures showing that both compounds inhibit the RNAP NAC by preventing RH-FL closure, thereby allosterically destabilizing the closed TL. This work reveals a conserved mechanistic principle of RNAP catalysis across all domains of life and provides new insight for antibiotic design.

PubMed: 41993335
DOI: 10.64898/2026.04.06.716786

実験手法

ELECTRON MICROSCOPY (2.9 Å)