DSSR-PyMOL cartoon-block schematics: PDB entry 9bs0

PDB-id

9bs0; DSSR-derived features in text and JSON formats

Class

ribosome

Method

cryo-EM (3.3 Å)

Summary

Yphc-treated 45syphc particle. class 5

Reference

Arpin D, Palacios A, Basu K, Ortega J (2025): "The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly." Nucleic Acids Res., 53. doi: 10.1093/nar/gkae1197.

Abstract

The intricate process of 50S ribosomal subunit assembly in Bacillus subtilis involves multiple parallel pathways converging into a crucial intermediate known as the 45S particle. RbgA and YphC, play pivotal roles in completing the maturation of the functional sites in the 45S particle. In this work, we found that RbgA and YphC can independently bind the 45S particle with high affinity, but when RbgA binds first to the particle, it significantly increases the binding affinity of YphC. Using cryo-electron microscopy, we determined that the changes exerted by RbgA and YphC when binding independently closely resemble those observed when the two factors bind to the 45S particle simultaneously. However, the structural analysis revealed that RbgA binding causes a conformational change that uncovers the binding site for YphC, thus increasing its binding affinity. We concluded that the functional interplay between RbgA and YphC primarily revolves around one factor promoting the binding of the other, rather than the binding of the two factors inducing entirely new conformational changes compared with those induced by the factors individually. These results highlight the synergic mechanism between two essential assembly factors, underscoring the intricate mechanism bacteria use to maximize the efficiency of the ribosome assembly process.