7PIT

70S ribosome with EF-G, A/P- and P/E-site tRNAs in pseudouridimycin-treated Mycoplasma pneumoniae cells

This is a non-PDB format compatible entry.

Summary for 7PIT

• Entry DOI: 10.2210/pdb7pit/pdb
• EMDB information: 13450
• Descriptor: 50S ribosomal protein L34, 30S ribosomal protein S7, 30S ribosomal protein S8, ... (55 entities in total)
• Functional Keywords: in-cell cryo-electron tomography, sub-tomogram analysis, ribosome, translation intermediate state, pseudouridimycin, translation
• Biological source: Mycoplasma pneumoniae M129; More
• Total number of polymer chains: 56
• Total formula weight: 2360665.77

Authors

Xue, L.,Lenz, S.,Rappsilber, J.,Mahamid, J. (deposition date: 2021-08-23, release date: 2022-05-25, Last modification date: 2024-11-06)

Primary citation

Xue, L.,Lenz, S.,Zimmermann-Kogadeeva, M.,Tegunov, D.,Cramer, P.,Bork, P.,Rappsilber, J.,Mahamid, J.
Visualizing translation dynamics at atomic detail inside a bacterial cell.
Nature, 610:205-211, 2022

PubMed Abstract: Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes. By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.

PubMed: 36171285
DOI: 10.1038/s41586-022-05255-2

Experimental method

ELECTRON MICROSCOPY (5.7 Å)