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Structure paper

TitleStructural basis of Rho-dependent transcription termination.
Journal, issue, pagesNature, Vol. 614, Issue 7947, Page 367-374, Year 2023
Publish dateJan 25, 2023
AuthorsVadim Molodtsov / Chengyuan Wang / Emre Firlar / Jason T Kaelber / Richard H Ebright /
PubMed AbstractRho 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 linksNature / PubMed:36697824 / PubMed Central
MethodsEM (single particle)
Resolution4.1 - 12.0 Å
Structure data

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

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

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

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

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

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

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

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

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

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 molecule*YM

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Source
  • escherichia coli (E. coli)
  • synthetic construct (others)
KeywordsTRANSCRIPTION / TRANSFERASE/DNA/RNA / factor-dependent termination / Rho / transcription termination / transcription elongation complex / helicase / ATPase / TRANSFERASE-DNA-RNA complex / TRANSCRIPTION/RNA / TRANSCRIPTION-RNA complex

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