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	Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 3186, Year 2024
Publish date	Apr 15, 2024
Authors	Nelly Said / Mark Finazzo / Tarek Hilal / Bing Wang / Tim Luca Selinger / Daniela Gjorgjevikj / Irina Artsimovitch / Markus C Wahl /
PubMed Abstract	Transcription termination factor ρ is a hexameric, RNA-dependent NTPase that can adopt active closed-ring and inactive open-ring conformations. The Sm-like protein Rof, a homolog of the RNA ...Transcription termination factor ρ is a hexameric, RNA-dependent NTPase that can adopt active closed-ring and inactive open-ring conformations. The Sm-like protein Rof, a homolog of the RNA chaperone Hfq, inhibits ρ-dependent termination in vivo but recapitulation of this activity in vitro has proven difficult and the precise mode of Rof action is presently unknown. Here, our cryo-EM structures of ρ-Rof and ρ-RNA complexes show that Rof undergoes pronounced conformational changes to bind ρ at the protomer interfaces, undercutting ρ conformational dynamics associated with ring closure and occluding extended primary RNA-binding sites that are also part of interfaces between ρ and RNA polymerase. Consistently, Rof impedes ρ ring closure, ρ-RNA interactions and ρ association with transcription elongation complexes. Structure-guided mutagenesis coupled with functional assays confirms that the observed ρ-Rof interface is required for Rof-mediated inhibition of cell growth and ρ-termination in vitro. Bioinformatic analyses reveal that Rof is restricted to Pseudomonadota and that the ρ-Rof interface is conserved. Genomic contexts of rof differ between Enterobacteriaceae and Vibrionaceae, suggesting distinct modes of Rof regulation. We hypothesize that Rof and other cellular anti-terminators silence ρ under diverse, but yet to be identified, stress conditions when unrestrained transcription termination by ρ may be detrimental.
External links	Nat Commun / PubMed:38622114 / PubMed Central
Methods	EM (single particle)
Resolution	2.7 - 3.3 Å
Structure data	17870 8ptg EMDB-17870, PDB-8ptg: Structure of the transcription termination factor Rho bound to RNA at the PBS and SBS Method: EM (single particle) / Resolution: 2.9 Å 17874 8ptm EMDB-17874, PDB-8ptm: Structure of the transcription termination factor Rho in complex with Rof and ADP Method: EM (single particle) / Resolution: 2.9 Å 17875 8ptn EMDB-17875, PDB-8ptn: Structure of the transcription termination factor Rho in complex with Rof Method: EM (single particle) / Resolution: 3.3 Å 17876 8pto EMDB-17876, PDB-8pto: Structure of Rho pentamer in complex with Rof and ADP Method: EM (single particle) / Resolution: 2.7 Å 17877 8ptp EMDB-17877, PDB-8ptp: Structure of Rho pentamer in complex with Rof Method: EM (single particle) / Resolution: 3.0 Å
Chemicals	ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-BEF*: BERYLLIUM TRIFLUORIDE ION
Source	escherichia coli (E. coli)
Keywords	TRANSCRIPTION / Transcription termination factor Rho Inhibition of termination Sm-like protein Rof Rho regulation / TRANSCRIPTION RNA binding PBS SBS / Transcription termination factor Rho Transcription inhibition Sm-like protein Rof Rho regulation