7ODE

E. coli 50S ribosome LiCl core particle

Summary for 7ODE

• Entry DOI: 10.2210/pdb7ode/pdb
• EMDB information: 12826
• Descriptor: 23S rRNA, 50S ribosomal protein L21, 50S ribosomal protein L22, ... (16 entities in total)
• Functional Keywords: ribosome assembly, folding, biogenesis, 50s, ribosome
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 16
• Total formula weight: 1152379.46

Authors

Larsson, D.S.D.,Selmer, M. (deposition date: 2021-04-29, release date: 2022-06-01, Last modification date: 2025-03-12)

Primary citation

Larsson, D.S.D.,Kanchugal P, S.,Selmer, M.
Structural Consequences of Deproteinating the 50S Ribosome.
Biomolecules, 12:-, 2022

PubMed Abstract: Ribosomes are complex ribonucleoprotein particles. Purified 50S ribosomes subjected to high-salt wash, removing a subset of ribosomal proteins (r-proteins), were shown as competent for in vitro assembly into functional 50S subunits. Here, we used cryo-EM to determine the structures of such LiCl core particles derived from 50S subunits. A wide range of complexes with large variations in the extent of the ordered 23S rRNA and the occupancy of r-proteins were resolved to between 2.8 Å and 9 Å resolution. Many of these particles showed high similarity to in vivo and in vitro assembly intermediates, supporting the inherent stability or metastability of these states. Similar to states in early ribosome assembly, the main class showed an ordered density for the particle base around the exit tunnel, with domain V and the 3'-half of domain IV disordered. In addition, smaller core particles were discovered, where either domain II or IV was unfolded. Our data support a multi-pathway in vitro disassembly process, similar but reverse to assembly. Dependencies between complex tertiary RNA structures and RNA-protein interactions were observed, where protein extensions dissociated before the globular domains. We observed the formation of a non-native RNA structure upon protein dissociation, demonstrating that r-proteins stabilize native RNA structures and prevent non-native interactions also after folding.

PubMed: 36358955
DOI: 10.3390/biom12111605

Experimental method

ELECTRON MICROSCOPY (2.84 Å)