7QIW

Specific features and methylation sites of a plant ribosome. 60S ribosomal subunit.

This is a non-PDB format compatible entry.

Summary for 7QIW

• Entry DOI: 10.2210/pdb7qiw/pdb
• EMDB information: 14001
• Descriptor: 60S ribosomal protein L8, 60S ribosomal protein uL5, 60S ribosomal protein L13, ... (51 entities in total)
• Functional Keywords: solanum lycopersicum, cytosolic ribosome, 80s, plant, rrna, ribosome
• Biological source: Solanum lycopersicum (tomato); More
• Total number of polymer chains: 45
• Total formula weight: 1992651.49

Authors

Cottilli, P.,Itoh, Y.,Amunts, A. (deposition date: 2021-12-16, release date: 2022-07-13, Last modification date: 2024-11-13)

Primary citation

Cottilli, P.,Itoh, Y.,Nobe, Y.,Petrov, A.S.,Lison, P.,Taoka, M.,Amunts, A.
Cryo-EM structure and rRNA modification sites of a plant ribosome.
Plant Commun., 3:100342-100342, 2022

PubMed Abstract: Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.

PubMed: 35643637
DOI: 10.1016/j.xplc.2022.100342

Experimental method

ELECTRON MICROSCOPY (2.35 Å)