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 of Rho-dependent transcription termination.
Journal, issue, pages	Nature, Vol. 614, Issue 7947, Page 367-374, Year 2023
Publish date	Jan 25, 2023
Authors	Vadim Molodtsov / Chengyuan Wang / Emre Firlar / Jason T Kaelber / Richard H Ebright /
PubMed Abstract	Rho is a ring-shaped hexameric ATP-dependent molecular motor. Together with the transcription elongation factor NusG, Rho mediates factor-dependent transcription termination and transcription- ...Rho is a ring-shaped hexameric ATP-dependent molecular motor. Together with the transcription elongation factor NusG, Rho mediates factor-dependent transcription termination and transcription-translation-coupling quality control in Escherichia coli. Here we report the preparation of complexes that are functional in factor-dependent transcription termination from Rho, NusG, RNA polymerase (RNAP), and synthetic nucleic acid scaffolds, and we report cryogenic electron microscopy structures of the complexes. The structures show that functional factor-dependent pre-termination complexes contain a closed-ring Rho hexamer; have RNA threaded through the central channel of Rho; have 60 nucleotides of RNA interacting sequence-specifically with the exterior of Rho and 6 nucleotides of RNA interacting sequence-specifically with the central channel of Rho; have Rho oriented relative to RNAP such that ATP-dependent translocation by Rho exerts mechanical force on RNAP; and have NusG bridging Rho and RNAP. The results explain five decades of research on Rho and provide a foundation for understanding Rho's function.
External links	Nature / PubMed:36697824 / PubMed Central
Methods	EM (single particle)
Resolution	4.1 - 12.0 Å
Structure data	27864 8e3f EMDB-27864, PDB-8e3f: Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, Mg-ADP-BeF3, and NusG; TEC part Method: EM (single particle) / Resolution: 6.5 Å 27865 8e3h EMDB-27865, PDB-8e3h: Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part Method: EM (single particle) / Resolution: 6.5 Å EMDB-27897: Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, Mg-ADP-BeF3, and NusG Method: EM (single particle) / Resolution: 12.0 Å 27913 8e5k EMDB-27913, PDB-8e5k: Escherichia coli Rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, Mg-ADP-BeF3, and NusG; TEC part Method: EM (single particle) / Resolution: 4.2 Å 27914 8e5l EMDB-27914, PDB-8e5l: Escherichia coli Rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part Method: EM (single particle) / Resolution: 4.2 Å EMDB-27915: Escherichia coli Rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, Mg-ADP-BeF3, and NusG Method: EM (single particle) / Resolution: 7.68 Å 27916 8e5o EMDB-27916, PDB-8e5o: Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG; TEC part Method: EM (single particle) / Resolution: 4.4 Å 27917 8e5p EMDB-27917, PDB-8e5p: Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part Method: EM (single particle) / Resolution: 4.4 Å EMDB-27918: Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG Method: EM (single particle) / Resolution: 8.8 Å 27928 8e6w EMDB-27928, PDB-8e6w: Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, lambda-tR1 rut RNA, Mg-ADP-BeF3, and NusG; Rho part Method: EM (single particle) / Resolution: 4.27 Å EMDB-27929: Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, lambda-tR1 rut RNA, Mg-ADP-BeF3, and NusG Method: EM (single particle) / Resolution: 6.41 Å 27930 8e6x EMDB-27930, PDB-8e6x: Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, lambda-tR1 rut RNA, Mg-ADP-BeF3, and NusG; TEC part Method: EM (single particle) / Resolution: 4.27 Å 27931 8e6z EMDB-27931, PDB-8e6z: Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, dC75 rut mimic RNA, Mg-ADP-BeF3, and NusG; TEC part Method: EM (single particle) / Resolution: 4.1 Å 27932 8e70 EMDB-27932, PDB-8e70: Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, dC75 rut mimic RNA, Mg-ADP-BeF3, and NusG; Rho hexamer part Method: EM (single particle) / Resolution: 4.1 Å EMDB-27933: Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, dC75 rut mimic RNA Method: EM (single particle) / Resolution: 4.1 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-BEF*: BERYLLIUM TRIFLUORIDE ION
Source	escherichia coli (E. coli) synthetic construct (others)
Keywords	TRANSCRIPTION / TRANSFERASE/DNA/RNA / factor-dependent termination / Rho / transcription termination / transcription elongation complex / helicase / ATPase / TRANSFERASE-DNA-RNA complex / TRANSCRIPTION/RNA / TRANSCRIPTION-RNA complex