9UWH

human mitoribosome trapped by retapamulin

This is a non-PDB format compatible entry.

Summary for 9UWH

• Entry DOI: 10.2210/pdb9uwh/pdb
• EMDB information: 64554
• Descriptor: 16S mitochondrial rRNA, Large ribosomal subunit protein uL14m, Large ribosomal subunit protein uL15m, ... (96 entities in total)
• Functional Keywords: mitoribosome, retapamulin, ribosome
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 86
• Total formula weight: 2939786.45

Authors

Ando, Y.,Nureki, O.,Itoh, Y. (deposition date: 2025-05-12, release date: 2025-10-29, Last modification date: 2025-12-10)

Primary citation

Wakigawa, T.,Mito, M.,Ando, Y.,Yamashiro, H.,Tomuro, K.,Tani, H.,Tomizawa, K.,Chujo, T.,Nagao, A.,Suzuki, T.,Nureki, O.,Wei, F.Y.,Shichino, Y.,Itoh, Y.,Suzuki, T.,Iwasaki, S.
Monitoring the complexity and dynamics of mitochondrial translation.
Mol.Cell, 85:4279-4297.e8, 2025

PubMed Abstract: Since mitochondrial translation leads to the synthesis of the essential oxidative phosphorylation (OXPHOS) subunits, exhaustive and quantitative delineation of mitoribosome traversal is needed. Here, we developed a variety of high-resolution mitochondrial ribosome profiling derivatives and revealed the intricate regulation of mammalian mitochondrial translation. Harnessing a translation inhibitor, retapamulin, our approach assessed the stoichiometry and kinetics of mitochondrial translation flux, such as the number of mitoribosomes on a transcript, the elongation rate, and the initiation rate. We also surveyed the impacts of modifications at the anticodon stem loop in mitochondrial tRNAs (mt-tRNAs), including all possible modifications at the 34th position, in cells deleting the corresponding enzymes and derived from patients, as well as in mouse tissues. Moreover, a retapamulin-assisted derivative and mito-disome profiling revealed mitochondrial translation initiation factor (mtIF) 3-mediated translation initiation from internal open reading frames (ORFs) and programmed mitoribosome collision sites across the mitochondrial transcriptome. Our work provides a useful platform for investigating protein synthesis within the energy powerhouse of the cell.

PubMed: 41232526
DOI: 10.1016/j.molcel.2025.10.022

Experimental method

ELECTRON MICROSCOPY (3 Å)