7UPH

Structure of a ribosome with tethered subunits

This is a non-PDB format compatible entry.

Summary for 7UPH

• Entry DOI: 10.2210/pdb7uph/pdb
• EMDB information: 26666
• Descriptor: 30S ribosomal protein S14, 5S rRNA, 50S ribosomal protein L2, ... (49 entities in total)
• Functional Keywords: engineered, tethered, synthetic, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 49
• Total formula weight: 2085073.85

Authors

Kim, D.S.,Watkins, A.,Bidstrup, E.,Lee, J.,Topkar, V.V.,Kofman, C.,Schwarz, K.J.,Liu, Y.,Pintilie, G.,Roney, E.,Das, R.,Jewett, M.C. (deposition date: 2022-04-15, release date: 2022-08-17, Last modification date: 2025-03-19)

Primary citation

Kim, D.S.,Watkins, A.,Bidstrup, E.,Lee, J.,Topkar, V.,Kofman, C.,Schwarz, K.J.,Liu, Y.,Pintilie, G.,Roney, E.,Das, R.,Jewett, M.C.
Three-dimensional structure-guided evolution of a ribosome with tethered subunits.
Nat.Chem.Biol., 18:990-998, 2022

PubMed Abstract: RNA-based macromolecular machines, such as the ribosome, have functional parts reliant on structural interactions spanning sequence-distant regions. These features limit evolutionary exploration of mutant libraries and confound three-dimensional structure-guided design. To address these challenges, we describe Evolink (evolution and linkage), a method that enables high-throughput evolution of sequence-distant regions in large macromolecular machines, and library design guided by computational RNA modeling to enable exploration of structurally stable designs. Using Evolink, we evolved a tethered ribosome with a 58% increased activity in orthogonal protein translation and a 97% improvement in doubling times in SQ171 cells compared to a previously developed tethered ribosome, and reveal new permissible sequences in a pair of ribosomal helices with previously explored biological function. The Evolink approach may enable enhanced engineering of macromolecular machines for new and improved functions for synthetic biology.

PubMed: 35836020
DOI: 10.1038/s41589-022-01064-w

Experimental method

ELECTRON MICROSCOPY (4.18 Å)