9MQ4

Damaged 70S ribosome with PrfH bound

This is a non-PDB format compatible entry.

Summary for 9MQ4

• Entry DOI: 10.2210/pdb9mq4/pdb
• EMDB information: 48513
• Descriptor: 23S ribosomal RNA, Large ribosomal subunit protein uL5, Large ribosomal subunit protein uL6, ... (60 entities in total)
• Functional Keywords: cgprfh, damaged ribosome, ribotoxin, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 58
• Total formula weight: 2265297.16

Authors

Tian, Y.,Li, Q.,Jin, H.,Fatma, S.,Zeng, F.,Huang, R.H. (deposition date: 2025-01-01, release date: 2025-02-05, Last modification date: 2025-03-19)

Primary citation

Tian, Y.,Li, Q.,Fatma, S.,Jiang, J.,Jin, H.,Zeng, F.,Huang, R.H.
Molecular and structural basis of a subfamily of PrfH rescuing both the damaged and intact ribosomes stalled in translation.
Biorxiv, 2025

PubMed Abstract: In bacteria, spontaneous mRNAs degradation and ribotoxin-induced RNA damage are two main biological events that lead to the stall of protein translation. The ubiquitous trans-translation system as well as several alternative rescue factors (Arfs) are responsible for rescuing the stalled ribosomes caused by truncated mRNAs that lack the stop codons. To date, protein release factor homolog (PrfH) is the only factor known to rescue the stalled ribosome damaged by ribotoxins. Here we show that a subfamily of PrfH, exemplified by PrfH from (PrfH), rescues both types of stalled ribosomes described above. Our biochemical assays demonstrate that PrfH hydrolyzes the peptides attached to P-site tRNAs when in complex with both the damaged and intact ribosomes. Two cryo-EM structures of PrfH in complex with the damaged and intact 70S ribosomes revealed that PrfH employs two different regions of the protein to recognize two different stalled ribosomes to orient the GGQ motif for peptide hydrolysis. Thus, using a combination of bioinformatic, biochemical, and structural characterization described here, we have uncovered a family of ribosome rescue factors that possesses dual activities to resolve two distinct stalled protein translation in bacteria.

PubMed: 39829893
DOI: 10.1101/2025.01.09.632186

Experimental method

ELECTRON MICROSCOPY (2.78 Å)