SNAP output for PDB entry 8e5k [SNAP web server]

PDB-id

8e5k; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription, transferase-DNA-RNA

Method

cryo-EM (4.2 Å)

Summary

Escherichia coli rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, mg-adp-bef3, and nusg; tec part

Reference

Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH (2023): "Structural basis of Rho-dependent transcription termination." Nature, 614, 367-374. doi: 10.1038/s41586-022-05658-1.

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-translation-coupling quality control in Escherichia coli_1-4. 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.