11BQ

Escherichia coli 70S ribosome containing an evolved 16S rRNA (EC-S3.5)

This is a non-PDB format compatible entry.

Summary for 11BQ

• Entry DOI: 10.2210/pdb11bq/pdb
• EMDB information: 75605
• Descriptor: 50S ribosomal protein L33, Small ribosomal subunit protein uS4, Small ribosomal subunit protein uS5, ... (59 entities in total)
• Functional Keywords: directed evolution, ribosome, translation
• Biological source: Escherichia coli; More
• Total number of polymer chains: 53
• Total formula weight: 2102454.33

Authors

Raskar, T.,Badran, A.,Fraser, J. (deposition date: 2026-02-16, release date: 2026-04-08)

Primary citation

Raskar, T.,Costello, A.,Badran, A.H.,Fraser, J.S.
Structural adaptations for enhanced translation kinetics in evolved ribosomes.
Biorxiv, 2026

PubMed Abstract: The ribosomal RNA sequence governs translation dynamics, yet understanding how changes beyond the conserved catalytic centers influence kinetics and protein yield remains limited. Using orthogonal ribosome phage-assisted continuous evolution (oRibo-PACE), we recently reported chimeric ribosomes derived from , , and endowed with elevated translation rates as compared to their starting counterparts. Here, we structurally characterize these kinetically enhanced ribosomes using cryo-electron microscopy and uncover a potential relationship between 16S rRNA stability and translation efficiency. Compared to their naive starting points, evolved ribosomes exhibit extensive RNA structural adaptation, often introduced by mismatches at key helical junctions, which leads to local RNA-protein rearrangements and destabilizes non-canonical base pairs. Compensatory mutations that restore base-pairing stability and eliminate flexibility reduced translational activity to wild-type levels. Across trajectories, increased translational output correlates with subtle, localized changes in the 16S rRNA sequence that introduce limited structural destabilization at specific elements. Taken together, our work provides new insights into rRNA structural malleability and establishes principles for engineering ribosomes with altered translation properties.

PubMed: 41846938
DOI: 10.64898/2026.03.05.706023

Experimental method

ELECTRON MICROSCOPY (3 Å)