SNAP output for PDB entry 7s9u [SNAP web server]

PDB-id

7s9u; SNAP-derived features in text and JSON formats; DNAproDB

Class

ribosome

Method

cryo-EM (3.2 Å)

Summary

44sr3c ribosomal particle

Reference

Seffouh A, Trahan C, Wasi T, Jain N, Basu K, Britton RA, Oeffinger M, Ortega J (2022): "RbgA ensures the correct timing in the maturation of the 50S subunits functional sites." Nucleic Acids Res., 50, 10801-10816. doi: 10.1093/nar/gkac059.

Abstract

RbgA is an essential protein for the assembly of the 50S subunit in Bacillus subtilis. Depletion of RbgA leads to the accumulation of the 45S intermediate. A strain expressing a RbgA variant with reduced GTPase activity generates spontaneous suppressor mutations in uL6. Each suppressor strain accumulates a unique 44S intermediate. We reasoned that characterizing the structure of these mutant 44S intermediates may explain why RbgA is required to catalyze the folding of the 50S functional sites. We found that in the 44S particles, rRNA helices H42 and H97, near the binding site of uL6, adopt a flexible conformation and allow the central protuberance and functional sites in the mutant 44S particles to mature in any order. Instead, the wild-type 45S particles exhibit a stable H42-H97 interaction and their functional sites always mature last. The dependence on RbgA was also less pronounced in the 44S particles. We concluded that the binding of uL6 pauses the maturation of the functional sites, but the central protuberance continues to fold. RbgA exclusively binds intermediates with a formed central protuberance and licenses the folding of the functional sites. Through this mechanism, RbgA ensures that the functional sites of the 50S mature last.