7OIZ

Cryo-EM structure of 70S ribosome stalled with TnaC peptide

This is a non-PDB format compatible entry.

Summary for 7OIZ

• Entry DOI: 10.2210/pdb7oiz/pdb
• EMDB information: 12936
• Descriptor: 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (59 entities in total)
• Functional Keywords: arrest peptide, translational stalling, gene regulation, translation termination, ribosome
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 55
• Total formula weight: 2120275.91

Authors

Su, T.,Kudva, R.,Becker, T.,Berninghausen, O.,Heijne, G.,Cheng, J.,Beckmann, R. (deposition date: 2021-05-13, release date: 2021-09-15, Last modification date: 2025-03-12)

Primary citation

Su, T.,Kudva, R.,Becker, T.,Buschauer, R.,Komar, T.,Berninghausen, O.,von Heijne, G.,Cheng, J.,Beckmann, R.
Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide.
Nucleic Acids Res., 49:9539-9547, 2021

PubMed Abstract: In Escherichia coli, elevated levels of free l-tryptophan (l-Trp) promote translational arrest of the TnaC peptide by inhibiting its termination. However, the mechanism by which translation-termination by the UGA-specific decoding release factor 2 (RF2) is inhibited at the UGA stop codon of stalled TnaC-ribosome-nascent chain complexes has so far been ambiguous. This study presents cryo-EM structures for ribosomes stalled by TnaC in the absence and presence of RF2 at average resolutions of 2.9 and 3.5 Å, respectively. Stalled TnaC assumes a distinct conformation composed of two small α-helices that act together with residues in the peptide exit tunnel (PET) to coordinate a single L-Trp molecule. In addition, while the peptidyl-transferase center (PTC) is locked in a conformation that allows RF2 to adopt its canonical position in the ribosome, it prevents the conserved and catalytically essential GGQ motif of RF2 from adopting its active conformation in the PTC. This explains how translation of the TnaC peptide effectively allows the ribosome to function as a L-Trp-specific small-molecule sensor that regulates the tnaCAB operon.

PubMed: 34403461
DOI: 10.1093/nar/gkab665

Experimental method

ELECTRON MICROSCOPY (2.9 Å)