7JT2

70S ribosome stalled on long mRNA with ArfB bound in the A site

This is a non-PDB format compatible entry.

Summary for 7JT2

• Entry DOI: 10.2210/pdb7jt2/pdb
• EMDB information: 22466 22469 22472
• Descriptor: 50S ribosomal protein L2, 50S ribosomal protein L15, 50S ribosomal protein L16, ... (55 entities in total)
• Functional Keywords: ribosome, arfb, mrna, translation
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 55
• Total formula weight: 2169919.33

Authors

Carbone, C.E.,Korostelev, A.A. (deposition date: 2020-08-16, release date: 2020-11-11, Last modification date: 2024-11-06)

Primary citation

Carbone, C.E.,Demo, G.,Madireddy, R.,Svidritskiy, E.,Korostelev, A.A.
ArfB can displace mRNA to rescue stalled ribosomes
Nat Commun, 11:5552-5552, 2020

PubMed Abstract: Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ribosomes stalled on mRNAs truncated at the A site, allowing ribosome recycling. Prior structural work revealed that ArfB recognizes such ribosomes by inserting its C-terminal α-helix into the vacant mRNA tunnel. In this work, we report that ArfB can efficiently recognize a wider range of mRNA substrates, including longer mRNAs that extend beyond the A-site codon. Single-particle cryo-EM unveils that ArfB employs two modes of function depending on the mRNA length. ArfB acts as a monomer to accommodate a shorter mRNA in the ribosomal A site. By contrast, longer mRNAs are displaced from the mRNA tunnel by more than 20 Å and are stabilized in the intersubunit space by dimeric ArfB. Uncovering distinct modes of ArfB function resolves conflicting biochemical and structural studies, and may lead to re-examination of other ribosome rescue pathways, whose functions depend on mRNA lengths.

PubMed: 33144582
DOI: 10.1038/s41467-020-19370-z

Experimental method

ELECTRON MICROSCOPY (3.5 Å)