9MSH

de novo SigN RNA polymerase open complex (RPo)

Summary for 9MSH

• Entry DOI: 10.2210/pdb9msh/pdb
• EMDB information: 48589
• Descriptor: DNA-directed RNA polymerase subunit alpha, ZINC ION, DNA-directed RNA polymerase subunit beta, ... (11 entities in total)
• Functional Keywords: sigma n, sigma 54, atpase, bacterial enhancer binding protein, transcription initiation, intermediate, transcription
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 500411.92

Authors

Mueller, A.U.,Darst, S.A. (deposition date: 2025-01-09, release date: 2025-08-13)

Primary citation

Mueller, A.U.,Molina, N.,Nixon, B.T.,Darst, S.A.
Real-time capture of sigma N transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding.
Nat Commun, 16:7138-7138, 2025

PubMed Abstract: Bacterial σ factors bind RNA polymerase (E) to form holoenzyme (Eσ), conferring promoter specificity to E and playing a key role in transcription bubble formation. σ is unique among σ factors in its structure and functional mechanism, requiring activation by specialized AAA+ ATPases. Eσ forms an inactive promoter complex where the N-terminal σ region I (σ-RI) threads through a small DNA bubble. On the opposite side of the DNA, the ATPase engages σ-RI within the pore of its hexameric ring. Here, we perform kinetics-guided structural analysis of de novo formed Eσ initiation complexes and engineer a biochemical assay to measure ATPase-mediated σ-RI translocation during promoter melting. We show that the ATPase exerts mechanical action to translocate about 30 residues of σ-RI through the DNA bubble, disrupting inhibitory structures of σ to allow full transcription bubble formation. A local charge switch of σ-RI from positive to negative may help facilitate disengagement of the otherwise processive ATPase, allowing subsequent σ disentanglement from the DNA bubble.

PubMed: 40759887
DOI: 10.1038/s41467-025-61837-4

Experimental method

ELECTRON MICROSCOPY (2.8 Å)