8G2W

Cryo-EM structure of 3DVA component 2 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand

Summary for 8G2W

• Entry DOI: 10.2210/pdb8g2w/pdb
• Related: 8F3C 8G0O 8G1S 8G4W 8G7E 8G8Z
• EMDB information: 28845 29640 29676 29683 29732 29812 29859
• Descriptor: DNA (39-MER), DNA (31-MER), DNA-directed RNA polymerase subunit alpha, ... (8 entities in total)
• Functional Keywords: rna polymerase, riboswitch, transcription, preq1
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 398536.23

Authors

Porta, J.C.,Chauvier, A.,Deb, I.,Ellinger, E.,Frank, A.T.,Meze, K.,Ohi, M.D.,Walter, N.G. (deposition date: 2023-02-06, release date: 2023-06-21, Last modification date: 2024-06-19)

Primary citation

Chauvier, A.,Porta, J.C.,Deb, I.,Ellinger, E.,Meze, K.,Frank, A.T.,Ohi, M.D.,Walter, N.G.
Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand.
Nat.Struct.Mol.Biol., 30:902-913, 2023

PubMed Abstract: Folding of nascent transcripts can be modulated by the RNA polymerase (RNAP) that carries out their transcription, and vice versa. A pause of RNAP during transcription of a preQ riboswitch (termed que-PEC) is stabilized by a previously characterized template consensus sequence and the ligand-free conformation of the nascent RNA. Ligand binding to the riboswitch induces RNAP pause release and downstream transcription termination; however, the mechanism by which riboswitch folding modulates pausing is unclear. Here, we report single-particle cryo-electron microscopy reconstructions of que-PEC in ligand-free and ligand-bound states. In the absence of preQ, the RNA transcript is in an unexpected hyper-translocated state, preventing downstream nucleotide incorporation. Strikingly, on ligand binding, the riboswitch rotates around its helical axis, expanding the surrounding RNAP exit channel and repositioning the transcript for elongation. Our study reveals the tight coupling by which nascent RNA structures and their ligands can functionally regulate the macromolecular transcription machinery.

PubMed: 37264140
DOI: 10.1038/s41594-023-01002-x

Experimental method

ELECTRON MICROSCOPY (3.7 Å)