7Y41

Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth

Summary for 7Y41

• Entry DOI: 10.2210/pdb7y41/pdb
• EMDB information: 33599
• Descriptor: 50S ribosomal subunit bL37, 50S ribosomal protein L11, 50S ribosomal protein L13, ... (35 entities in total)
• Functional Keywords: mycobacterium 50s subunit, domain iv of 23s rrna, log phase, ribosome
• Biological source: Mycolicibacterium smegmatis MC2 155; More
• Total number of polymer chains: 33
• Total formula weight: 1479788.32

Authors

Sengupta, J.,Baid, P. (deposition date: 2022-06-13, release date: 2023-05-03, Last modification date: 2024-05-15)

Primary citation

Baid, P.,Sengupta, J.
Cryo-EM captures a unique conformational rearrangement in 23S rRNA helices of the Mycobacterium 50S subunit.
Int.J.Biol.Macromol., 253:126876-126876, 2023

PubMed Abstract: Structural investigations of the ribosomes isolated from pathogenic and non-pathogenic Mycobacterium species have identified several mycobacteria-specific structural features of ribosomal RNA and proteins. Here, we report structural evidence of a hitherto unknown conformational switch of mycobacterium 23S rRNA helices (H54a and H67-H71). Cryo-electron microscopy (cryo-EM) structures (~3-4 Å) of the M. smegmatis (Msm) log-phase 50S ribosomal subunit revealed conformational variability in H67-H71 region of the 23S rRNA, and manifested that, while H68 possesses the usual stretched conformation in one class of the maps, another one exhibits a bulge-out, fused density of H68-H69 at the inter-subunit surface, indicating an intrinsic dynamics of these rRNA helices. Remarkably, altered conformation of H68 forming a more prominent bulge-out structure at the inter-subunit surface of the 50S subunit due to the conformational rearrangements of 23S rRNA H67-H71 region was clearly visualized in a 3 Å cryo-EM map of the 50S subunit obtained from the stationary phase ribosome dataset. The Msm50S subunit having such bulge-out conformation at the intersubunit surface would be incompatible for associating with the 30S subunit due to its inability to form major inter-subunit bridges. Evidently, availability of active 70S ribosome pool can be modulated by stabilizing either one of the H68 conformation.

PubMed: 37709237
DOI: 10.1016/j.ijbiomac.2023.126876

Experimental method

ELECTRON MICROSCOPY (4.1 Å)