9M7Z

Cryo-EM structure of gp79 bound RNAP core enzyme

This is a non-PDB format compatible entry.

Summary for 9M7Z

• Entry DOI: 10.2210/pdb9m7z/pdb
• EMDB information: 63698
• Descriptor: DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', DNA-directed RNA polymerase subunit alpha, ... (5 entities in total)
• Functional Keywords: phage, transcription regulation, sigma factor, gp79, gp36, transcription
• Biological source: Escherichia coli; More
• Total number of polymer chains: 6
• Total formula weight: 399115.63

Authors

Xu, L.,Feng, Y. (deposition date: 2025-03-11, release date: 2025-09-03)

Primary citation

Xu, L.,Liang, L.,Yuan, L.,Yao, Y.,Hua, X.,Feng, Y.
A phage transcription factor displaces the host sigma factor and stabilizes its own sigma factor.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Phages are the most abundant self-replicating entities on earth, and understanding their transcriptional regulation can provide insights into bacterial gene expression mechanisms. The bacterial RNA polymerase core enzyme interacts with various σ factors to recognize and unwind promoter DNA. Gp79, a protein from Escherichia coli phage phiEco32, inhibits host σ70-mediated transcription while simultaneously activating transcription through its own σ factor, gp36. The underlying mechanism of this unusual dual regulatory role has remained unclear. In this study, we present cryo-EM structures of E. coli RNA polymerase (RNAP) in complex with gp79, and of RNAP in complex with gp79, gp36, and a cognate promoter. Structural and biochemical analyses reveal the basis for σ displacement by gp79 and promoter recognition by gp36. Our findings show that the N-terminus of gp79 invades the RNA channel, effectively displacing σ4. Upon encountering gp36, the N-terminus of gp79 adopts a new conformation, binds to gp36, and stabilizes the RNAP-promoter open complex. These findings advance our understanding of phage transcriptional regulation and suggest potential applications for synthetic biology.

PubMed: 40682819
DOI: 10.1093/nar/gkaf683

Experimental method

ELECTRON MICROSCOPY (5.5 Å)