SNAP output for PDB entry 8wi8 [SNAP web server]

PDB-id

8wi8; SNAP-derived features in text and JSON formats; DNAproDB

Class

ribosome

Method

cryo-EM (2.7 Å)

Summary

Cryo- em structure of mycobacterium smegmatis 50s ribosomal subunit (body 1) of 70s ribosome, bs1 and rafh.

Reference

Kumar N, Sharma S, Kaushal PS (2024): "Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH." Nat Commun, 15, 638. doi: 10.1038/s41467-024-44879-y.

Abstract

Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium tuberculosis encounters hypoxia (low oxygen) as a major stress in the host macrophages, and upregulates the expression of RafH protein, which is crucial for its survival. The RafH, a dual domain HPF, an orthologue of bacterial long HPF (HPF_long), hibernates ribosome in 70S monosome form, whereas in other bacteria, the HPF_long induces 70S ribosome dimerization and hibernates its ribosome in 100S disome form. Here, we report the cryo- EM structure of M. smegmatis, a close homolog of M. tuberculosis, 70S ribosome in complex with the RafH factor at an overall 2.8 Å resolution. The N- terminus domain (NTD) of RafH binds to the decoding center, similarly to HPF_long NTD. In contrast, the C- terminus domain (CTD) of RafH, which is larger than the HPF_long CTD, binds to a distinct site at the platform binding center of the ribosomal small subunit. The two domain-connecting linker regions, which remain mostly disordered in earlier reported HPF_long structures, interact mainly with the anti-Shine Dalgarno sequence of the 16S rRNA.