6H58

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome

This is a non-PDB format compatible entry.

Summary for 6H58

• Entry DOI: 10.2210/pdb6h58/pdb
• Related: 6H4N
• EMDB information: 0137 0139
• Descriptor: 50S ribosomal protein L32, 50S ribosomal protein L3, 50S ribosomal protein L4, ... (56 entities in total)
• Functional Keywords: 100s, cryo-em, e-site trna, hibernation, hpf, ribosome, rmf, s1
• Biological source: Escherichia coli BW25113; More
• Total number of polymer chains: 112
• Total formula weight: 4434579.60

Authors

Beckert, B.,Turk, M.,Czech, A.,Berninghausen, O.,Beckmann, R.,Ignatova, Z.,Plitzko, J.,Wilson, D.N. (deposition date: 2018-07-24, release date: 2018-09-05, Last modification date: 2024-10-09)

Primary citation

Beckert, B.,Turk, M.,Czech, A.,Berninghausen, O.,Beckmann, R.,Ignatova, Z.,Plitzko, J.M.,Wilson, D.N.
Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1.
Nat Microbiol, 3:1115-1121, 2018

PubMed Abstract: To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF). Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria, and reveals a unique role for bS1 in translation regulation.

PubMed: 30177741
DOI: 10.1038/s41564-018-0237-0

Experimental method

ELECTRON MICROSCOPY (7.9 Å)