8WIC

Cryo- EM structure of Mycobacterium smegmatis 50S ribosomal subunit (body 1) of 70S ribosome, E- tRNA and RafH.

Summary for 8WIC

• Entry DOI: 10.2210/pdb8wic/pdb
• EMDB information: 37563
• Descriptor: 50S ribosomal protein L2, 50S ribosomal protein L17, 50S ribosomal protein L18, ... (29 entities in total)
• Functional Keywords: ribosome, protein synthesis, mycobacterium smegmatis, hibernation promotion factor, hpf, rafh, hypoxia stress, cryo- em, single particle reconstruction
• Biological source: Mycolicibacterium smegmatis MC2 155; More
• Total number of polymer chains: 29
• Total formula weight: 1431156.13

Authors

Kumar, N.,Sharma, S.,Kaushal, P.S. (deposition date: 2023-09-24, release date: 2024-02-28)

Primary citation

Kumar, N.,Sharma, S.,Kaushal, P.S.
Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH.
Nat Commun, 15:638-638, 2024

PubMed 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), hibernates ribosome in 70S monosome form, whereas in other bacteria, the HPF 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 NTD. In contrast, the C- terminus domain (CTD) of RafH, which is larger than the HPF 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 structures, interact mainly with the anti-Shine Dalgarno sequence of the 16S rRNA.

PubMed: 38245551
DOI: 10.1038/s41467-024-44879-y

Experimental method

ELECTRON MICROSCOPY (3.5 Å)