7JIL

70S ribosome Flavobacterium johnsoniae

This is a non-PDB format compatible entry.

Summary for 7JIL

• Entry DOI: 10.2210/pdb7jil/pdb
• EMDB information: 22345
• Descriptor: 50S ribosomal protein L2, 50S ribosomal protein L16, 50S ribosomal protein L17, ... (54 entities in total)
• Functional Keywords: translation initiation, protein synthesis, bs21, ribosome
• Biological source: Flavobacterium johnsoniae; More
• Total number of polymer chains: 53
• Total formula weight: 2137364.67

Authors

Ortega, J. (deposition date: 2020-07-23, release date: 2020-12-02, Last modification date: 2024-05-15)

Primary citation

Jha, V.,Roy, B.,Jahagirdar, D.,McNutt, Z.A.,Shatoff, E.A.,Boleratz, B.L.,Watkins, D.E.,Bundschuh, R.,Basu, K.,Ortega, J.,Fredrick, K.
Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.
Nucleic Acids Res., 49:547-567, 2021

PubMed Abstract: Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the Bacteroidetes, fail to recognize the SD sequence of mRNA in vitro. A cryo-electron microscopy structure of the complete 70S ribosome from F. johnsoniae at 2.8 Å resolution reveals that the ASD is sequestered by ribosomal proteins bS21, bS18 and bS6, explaining the basis of ASD inhibition. The structure also uncovers a novel ribosomal protein-bL38. Remarkably, in F. johnsoniae and many other Flavobacteriia, the gene encoding bS21 contains a strong SD, unlike virtually all other genes. A subset of Flavobacteriia have an alternative ASD, and in these organisms the fully complementary sequence lies upstream of the bS21 gene, indicative of natural covariation. In other Bacteroidetes classes, strong SDs are frequently found upstream of the genes for bS21 and/or bS18. We propose that these SDs are used as regulatory elements, enabling bS21 and bS18 to translationally control their own production.

PubMed: 33330920
DOI: 10.1093/nar/gkaa1195

Experimental method

ELECTRON MICROSCOPY (2.8 Å)