Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 30, Issue 7, Page 902-913, Year 2023
Publish date	Jun 1, 2023
Authors	Adrien Chauvier / Jason C Porta / Indrajit Deb / Emily Ellinger / Katarina Meze / Aaron T Frank / Melanie D Ohi / Nils G Walter /
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 ...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.
External links	Nat Struct Mol Biol / PubMed:37264140 / PubMed Central
Methods	EM (single particle)
Resolution	3.4 - 4.3 Å
Structure data	28845 8f3c EMDB-28845, PDB-8f3c: Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Method: EM (single particle) / Resolution: 3.4 Å 29640 8g00 EMDB-29640, PDB-8g00: Cryo-EM structure of 3DVA component 0 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Method: EM (single particle) / Resolution: 3.4 Å 29676 8g1s EMDB-29676, PDB-8g1s: Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Method: EM (single particle) / Resolution: 3.7 Å 29683 8g2w EMDB-29683, PDB-8g2w: Cryo-EM structure of 3DVA component 2 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Method: EM (single particle) / Resolution: 3.7 Å 29732 8g4w EMDB-29732, PDB-8g4w: Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand Method: EM (single particle) / Resolution: 3.8 Å 29812 8g7e EMDB-29812, PDB-8g7e: Cryo-EM structure of 3DVA component 0 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand Method: EM (single particle) / Resolution: 3.9 Å 29859 8g8z EMDB-29859, PDB-8g8z: Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand Method: EM (single particle) / Resolution: 4.3 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-PRF: 7-DEAZA-7-AMINOMETHYL-GUANINE
Source	escherichia coli (E. coli) bacillus subtilis (bacteria)
Keywords	TRANSCRIPTION / RNA Polymerase / Riboswitch / preQ1 / Polymerase / RNAP / aptamer