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 insights into RNA-mediated transcription regulation in bacteria.
Journal, issue, pages	Mol Cell, Vol. 82, Issue 20, Page 3885-3900.e10, Year 2022
Publish date	Oct 20, 2022
Authors	Sanjay Dey / Claire Batisse / Jinal Shukla / Michael W Webster / Maria Takacs / Charlotte Saint-André / Albert Weixlbaumer /
PubMed Abstract	RNA can regulate its own synthesis without auxiliary proteins. For example, U-rich RNA sequences signal RNA polymerase (RNAP) to pause transcription and are required for transcript release at ...RNA can regulate its own synthesis without auxiliary proteins. For example, U-rich RNA sequences signal RNA polymerase (RNAP) to pause transcription and are required for transcript release at intrinsic terminators in all kingdoms of life. In contrast, the regulatory RNA putL suppresses pausing and termination in cis. However, how nascent RNA modulates its own synthesis remains largely unknown. We present cryo-EM reconstructions of RNAP captured during transcription of putL variants or an unrelated sequence at a U-rich pause site. Our results suggest how putL suppresses pausing and promotes its synthesis. We demonstrate that transcribing a U-rich sequence, a ubiquitous trigger of intrinsic termination, promotes widening of the RNAP nucleic-acid-binding channel. Widening destabilizes RNAP interactions with DNA and RNA to facilitate transcript dissociation reminiscent of intrinsic transcription termination. Surprisingly, RNAP remains bound to DNA after transcript release. Our results provide the structural framework to understand RNA-mediated intrinsic transcription termination.
External links	Mol Cell / PubMed:36220101
Methods	EM (single particle)
Resolution	3.4 - 4.5 Å
Structure data	15327 8aby EMDB-15327, PDB-8aby: RNA polymerase bound to purified in vitro transcribed regulatory RNA putL - pause prone, closed clamp state Method: EM (single particle) / Resolution: 3.7 Å 15328 8abz EMDB-15328, PDB-8abz: RNA polymerase at U-rich pause bound to non-regulatory RNA - pause prone, closed clamp state Method: EM (single particle) / Resolution: 3.4 Å 15329 8ac0 EMDB-15329, PDB-8ac0: RNA polymerase at U-rich pause bound to regulatory RNA putL - active, closed clamp state Method: EM (single particle) / Resolution: 4.1 Å 15330 8ac1 EMDB-15330, PDB-8ac1: RNA polymerase at U-rich pause bound to non-regulatory RNA - inactive, open clamp state Method: EM (single particle) / Resolution: 4.06 Å 15331 8ac2 EMDB-15331, PDB-8ac2: RNA polymerase- post-terminated, open clamp state Method: EM (single particle) / Resolution: 3.7 Å 15352 8acp EMDB-15352, PDB-8acp: RNA polymerase at U-rich pause bound to regulatory RNA putL - inactive, open clamp state Method: EM (single particle) / Resolution: 4.5 Å 15357 8ad1 EMDB-15357, PDB-8ad1: RNA polymerase at U-rich pause bound to RNA putL triple mutant - pause prone, closed clamp state Method: EM (single particle) / Resolution: 4.1 Å EMDB-15612: RNA polymerase at U-rich pause bound to regulatory RNA putL - Pause-prone, closed clamp state Method: EM (single particle) / Resolution: 4.28 Å EMDB-15613: RNA polymerase bound to purified in vitro transcribed regulatory RNA putL - inactive, open clamp state Method: EM (single particle) / Resolution: 4.4 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry
Source	escherichia coli k-12 (bacteria) escherichia coli (E. coli) escherichia coli bl21 (bacteria)
Keywords	TRANSCRIPTION / RNA polymerase / transcriptional pausing / transcription termination / regulatory RNA