7QI5

Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A resolution

This is a non-PDB format compatible entry.

Summary for 7QI5

• Entry DOI: 10.2210/pdb7qi5/pdb
• EMDB information: 13981
• Descriptor: 12S mitochondrial rRNA, 28S ribosomal protein S12, mitochondrial, VALINE, ... (101 entities in total)
• Functional Keywords: ribosome, mitochondrial translation, trna, mrna, 2fe-2s clusters, polyamines, rrna modifications, post-translation modifications, cryo em
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 94
• Total formula weight: 3136519.25

Authors

Singh, V.,Itoh, Y.,Amunts, A. (deposition date: 2021-12-14, release date: 2023-07-05, Last modification date: 2024-07-31)

Primary citation

Singh, V.,Itoh, Y.,Del'Olio, S.,Hassan, A.,Naschberger, A.,Flygaard, R.K.,Nobe, Y.,Izumikawa, K.,Aibara, S.,Andrell, J.,Whitford, P.C.,Barrientos, A.,Taoka, M.,Amunts, A.
Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.
Nat Commun, 15:4272-4272, 2024

PubMed Abstract: The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide a description of the structure and function of the human mitoribosome.

PubMed: 38769321
DOI: 10.1038/s41467-024-48163-x

Experimental method

ELECTRON MICROSCOPY (2.63 Å)