9MSE
de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic bEBP state (RPi1 open ring)
Summary for 9MSE
| Entry DOI | 10.2210/pdb9mse/pdb |
| EMDB information | 48586 |
| Descriptor | Transcriptional regulator (NtrC family), MAGNESIUM ION, PYROPHOSPHATE 2-, ... (13 entities in total) |
| Functional Keywords | sigma n, sigma 54, atpase, bacterial enhancer binding protein, transcription initiation, intermediate, transcription |
| Biological source | Aquifex aeolicus VF5 More |
| Total number of polymer chains | 16 |
| Total formula weight | 743403.82 |
| Authors | |
| 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 Cited by 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: 40759887DOI: 10.1038/s41467-025-61837-4 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.7 Å) |
Structure validation
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