6YST

Structure of the P+9 ArfB-ribosome complex with P/E hybrid tRNA in the post-hydrolysis state

This is a non-PDB format compatible entry.

Summary for 6YST

• Entry DOI: 10.2210/pdb6yst/pdb
• EMDB information: 10907
• Descriptor: 50S ribosomal protein L32, 50S ribosomal protein L2, 50S ribosomal protein L3, ... (61 entities in total)
• Functional Keywords: translation, ribosome, rescue, release
• Biological source: Escherichia coli; More
• Total number of polymer chains: 58
• Total formula weight: 2225761.91

Authors

Chan, K.-H.,Petrychenko, V.,Mueller, C.,Maracci, C.,Holtkamp, W.,Wilson, D.N.,Fischer, N.,Rodnina, M.V. (deposition date: 2020-04-23, release date: 2020-08-19, Last modification date: 2025-03-12)

Primary citation

Chan, K.H.,Petrychenko, V.,Mueller, C.,Maracci, C.,Holtkamp, W.,Wilson, D.N.,Fischer, N.,Rodnina, M.V.
Mechanism of ribosome rescue by alternative ribosome-rescue factor B.
Nat Commun, 11:4106-4106, 2020

PubMed Abstract: Alternative ribosome-rescue factor B (ArfB) rescues ribosomes stalled on non-stop mRNAs by releasing the nascent polypeptide from the peptidyl-tRNA. By rapid kinetics we show that ArfB selects ribosomes stalled on short truncated mRNAs, rather than on longer mRNAs mimicking pausing on rare codon clusters. In combination with cryo-electron microscopy we dissect the multistep rescue pathway of ArfB, which first binds to ribosomes very rapidly regardless of the mRNA length. The selectivity for shorter mRNAs arises from the subsequent slow engagement step, as it requires longer mRNA to shift to enable ArfB binding. Engagement results in specific interactions of the ArfB C-terminal domain with the mRNA entry channel, which activates peptidyl-tRNA hydrolysis by the N-terminal domain. These data reveal how protein dynamics translate into specificity of substrate recognition and provide insights into the action of a putative rescue factor in mitochondria.

PubMed: 32796827
DOI: 10.1038/s41467-020-17853-7

Experimental method

ELECTRON MICROSCOPY (3.2 Å)