9MSG

De novo SigN RNA polymerase transcription initiation intermediate with bound SigN-RII

Summary for 9MSG

• Entry DOI: 10.2210/pdb9msg/pdb
• EMDB information: 48588
• Descriptor: Transcriptional regulator (NtrC family), MAGNESIUM ION, ADENOSINE-5'-DIPHOSPHATE, ... (14 entities in total)
• Functional Keywords: sigma n, sigma 54, atpase, bacterial enhancer binding protein, transcription initiation, intermediate, transcription, transferase-dna complex, transferase/dna
• Biological source: Aquifex aeolicus VF5; More
• Total number of polymer chains: 14
• Total formula weight: 687788.92

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 (2.7 Å)