7CPJ

ycbZ-stalled 70S ribosome

This is a non-PDB format compatible entry.

Summary for 7CPJ

• Entry DOI: 10.2210/pdb7cpj/pdb
• EMDB information: 30431
• Descriptor: 16S ribosomal RNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (58 entities in total)
• Functional Keywords: ribosome, antibiotic
• Biological source: Escherichia coli; More
• Total number of polymer chains: 56
• Total formula weight: 2197799.22

Authors

Yokoyama, T.,Shirouzu, M.,Ito, T. (deposition date: 2020-08-07, release date: 2021-12-08, Last modification date: 2025-02-12)

Primary citation

Fujita, T.,Yokoyama, T.,Shirouzu, M.,Taguchi, H.,Ito, T.,Iwasaki, S.
The landscape of translational stall sites in bacteria revealed by monosome and disome profiling.
Rna, 28:290-302, 2022

PubMed Abstract: Ribosome pauses are associated with various cotranslational events and determine the fate of mRNAs and proteins. Thus, the identification of precise pause sites across the transcriptome is desirable; however, the landscape of ribosome pauses in bacteria remains ambiguous. Here, we harness monosome and disome (or collided ribosome) profiling strategies to survey ribosome pause sites in Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences: a low frequency of disomes at stop codons, collisions occurring immediately after 70S assembly on start codons, and shorter queues of ribosomes trailing upstream. The pause sites corresponded with the biochemical validation by integrated nascent chain profiling (iNP) to detect polypeptidyl-tRNA, an elongation intermediate. Moreover, the subset of those sites showed puromycin resistance, presenting slow peptidyl transfer. Among the identified sites, the ribosome pause at Asn586 of was validated by biochemical reporter assay, tRNA sequencing (tRNA-seq), and cryo-electron microscopy (cryo-EM) experiments. Our results provide a useful resource for ribosome stalling sites in bacteria.

PubMed: 34906996
DOI: 10.1261/rna.078188.120

Experimental method

ELECTRON MICROSCOPY (3.3 Å)