9YXB

Babesia divergens ribosome structure by single-particle cryo-EM (3D class1, A-, P-, and E-site tRNAs and mRNA)

This is a non-PDB format compatible entry.

Summary for 9YXB

• Entry DOI: 10.2210/pdb9yxb/pdb
• EMDB information: 73602
• Descriptor: 40S ribosomal protein uS12, 40S ribosomal protein uS8, 40S ribosomal protein eS7, ... (84 entities in total)
• Functional Keywords: trnas, rna modification, 80s, ribosome
• Biological source: Babesia divergens; More
• Total number of polymer chains: 82
• Total formula weight: 3162974.47

Authors

Gutierrez-Vargas, C.,Izhaki-Tavor, L.S.,Leger-Abraham, M. (deposition date: 2025-10-27, release date: 2026-06-24, Last modification date: 2026-07-01)

Primary citation

Gutierrez-Vargas, C.,Izhaki-Tavor, L.S.,Calvopina-Chavez, D.,Keroack, C.D.,Copello, P.,Duraisingh, M.T.,Leger-Abraham, M.
Ribosomal Architecture and rRNA Modification Landscape in the Tick-Borne Parasite Babesia divergens.
Biorxiv, 2025

PubMed Abstract: is a tick-borne intracellular apicomplexan parasite responsible for diseases ranging from mild to fatal, with a broadening geographic distribution. Due to the complex life cycle of species, their survival depends on the precise control of gene expression, which is primarily regulated by epigenetic, transcriptional, and post-transcriptional mechanisms. High-resolution structural information on key components of the translation machinery, such as ribosomes, could aid in the development of antiparasitic drugs. Here, we report cryo-EM ribosome structures (2.6 Å) from the tick-borne apicomplexan pathogen , showing associated tRNAs, an mRNA fragment, and RACK1, a signaling scaffold crucial to translation regulation. Density map analysis displays ribosome regions at atomic resolution (1.7 Å), which, when combined with nanopore sequencing, enabled the comprehensive identification of rRNA modifications, including modifications unreported in other organisms. The new rRNA modifications localize not only to the reduced rRNA expansion segments but also to functionally essential ribosomal sites, uncovering new avenues for therapeutic intervention against babesiosis.

PubMed: 41293005
DOI: 10.1101/2025.11.11.687446

Experimental method

ELECTRON MICROSCOPY (3.1 Å)