Journal: Nat Plants / Year: 2020 Title: Cryo-EM structure of the RNA-rich plant mitochondrial ribosome. Authors: Florent Waltz / Heddy Soufari / Anthony Bochler / Philippe Giegé / Yaser Hashem / Abstract: The vast majority of eukaryotic cells contain mitochondria, essential powerhouses and metabolic hubs. These organelles have a bacterial origin and were acquired during an early endosymbiosis event. ...The vast majority of eukaryotic cells contain mitochondria, essential powerhouses and metabolic hubs. These organelles have a bacterial origin and were acquired during an early endosymbiosis event. Mitochondria possess specialized gene expression systems composed of various molecular machines, including the mitochondrial ribosomes (mitoribosomes). Mitoribosomes are in charge of translating the few essential mRNAs still encoded by mitochondrial genomes. While chloroplast ribosomes strongly resemble those of bacteria, mitoribosomes have diverged significantly during evolution and present strikingly different structures across eukaryotic species. In contrast to animals and trypanosomatids, plant mitoribosomes have unusually expanded ribosomal RNAs and have conserved the short 5S rRNA, which is usually missing in mitoribosomes. We have previously characterized the composition of the plant mitoribosome, revealing a dozen plant-specific proteins in addition to the common conserved mitoribosomal proteins. In spite of the tremendous recent advances in the field, plant mitoribosomes remained elusive to high-resolution structural investigations and the plant-specific ribosomal features of unknown structures. Here, we present a cryo-electron microscopy study of the plant 78S mitoribosome from cauliflower at near-atomic resolution. We show that most of the plant-specific ribosomal proteins are pentatricopeptide repeat proteins (PPRs) that deeply interact with the plant-specific rRNA expansion segments. These additional rRNA segments and proteins reshape the overall structure of the plant mitochondrial ribosome, and we discuss their involvement in the membrane association and mRNA recruitment prior to translation initiation. Finally, our structure unveils an rRNA-constructive phase of mitoribosome evolution across eukaryotes.
History
Deposition
Jan 31, 2020
-
Header (metadata) release
Apr 15, 2020
-
Map release
Apr 15, 2020
-
Update
Apr 29, 2020
-
Current status
Apr 29, 2020
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Macromolecule #63: Translation elongation factor EF1B/ribosomal protein S6 family protein
Macromolecule
Name: Translation elongation factor EF1B/ribosomal protein S6 family protein type: protein_or_peptide / ID: 63 / Number of copies: 1 / Enantiomer: LEVO
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi