10MB

Open1 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL)

Summary for 10MB

• Entry DOI: 10.2210/pdb10mb/pdb
• EMDB information: 75280
• Descriptor: DNA, ZINC ION, DNA-directed RNA polymerase subunit omega, ... (11 entities in total)
• Functional Keywords: transcription, nucleotide addition cycle, dna/rna, transcription-dna-rna complex, transcription/dna/rna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 415976.78

Authors

Dhingra, Y.,Darst, S.A. (deposition date: 2026-01-27, release date: 2026-04-29)

Primary citation

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

Experimental method

ELECTRON MICROSCOPY (2.9 Å)