- EMDB-15773: Cryo-EM structure of the plant 60S subunit -
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Basic information
Entry
Database: EMDB / ID: EMD-15773
Title
Cryo-EM structure of the plant 60S subunit
Map data
The large subunit of the tobacco ribosome from cytosol
Sample
Complex: 40S subunit of the cytosolic 80S ribosome from tobacco
RNA: x 1 types
Protein or peptide: x 34 types
RNA: x 2 types
Protein or peptide: x 9 types
Ligand: x 6 types
Keywords
Plant / 80S / rRNA Modifications / ribosome
Function / homology
Function and homology information
protein-RNA complex assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding ...protein-RNA complex assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / metal ion binding Similarity search - Function
Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L41 / Ribosomal protein L41 / metallochaperone-like domain / TRASH domain ...Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L41 / Ribosomal protein L41 / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L30/YlxQ / 60S ribosomal protein L35 / Ribosomal Protein L6, KOW domain / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L7A/L8 / Ribosomal protein L6e / 60S ribosomal protein L6E / Ribosomal protein L18e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L37ae / Ribosomal protein L7, eukaryotic / Ribosomal protein L31e, conserved site / Ribosomal L37ae protein family / Ribosomal protein L31e signature. / Ribosomal_L19e / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L39e / Ribosomal protein L14e domain / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L14 / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L14 / Ribosomal protein L6, conserved site-2 Similarity search - Domain/homology
60S ribosomal protein L35-like / 60S ribosomal protein L30-like / Ribosomal protein L19 / 60S ribosomal protein L4-like / 60S ribosomal protein L37a / 60S ribosomal protein L11-1 / 60S ribosomal protein L21-1-like / 60S ribosomal protein L5-like / 60S ribosomal protein L23 / 60S ribosomal protein L35a-3 ...60S ribosomal protein L35-like / 60S ribosomal protein L30-like / Ribosomal protein L19 / 60S ribosomal protein L4-like / 60S ribosomal protein L37a / 60S ribosomal protein L11-1 / 60S ribosomal protein L21-1-like / 60S ribosomal protein L5-like / 60S ribosomal protein L23 / 60S ribosomal protein L35a-3 / 60S ribosomal protein L8-like / 60S ribosomal protein L31 / 60S ribosomal protein L29 / 60S ribosomal protein L39-3 / 60S ribosomal protein L10-like / 60S ribosomal protein L32-1 / 60S ribosomal protein L3 / 60S ribosomal protein L7-4-like / 60S ribosomal protein L14-1 / 60S ribosomal protein L27 / 60S ribosomal protein L44 / 60S ribosomal protein L6-like isoform X1 / 60S ribosomal protein L27a-3-like / 60S ribosomal protein L24-like / 60S ribosomal protein L22-2-like / 60S ribosomal protein L9-1-like / 60S ribosomal protein L38 / 60S ribosomal protein L17-1-like / 60S ribosomal protein L18a / 60S ribosomal protein L13 / 60S ribosomal protein L28-1-like / 60S ribosomal protein L36 / Ribosomal protein L15 / 60S ribosomal protein L7a / 60S ribosomal protein L18-2-like / 60S ribosomal protein L13a-4 / Ribosomal protein L37 / 60S ribosomal protein L26-1-like / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL23 Similarity search - Component
Biological species
Nicotiana tabacum (common tobacco)
Method
single particle reconstruction / cryo EM / Resolution: 2.14 Å
Journal: Nat Plants / Year: 2023 Title: Structure of the actively translating plant 80S ribosome at 2.2 Å resolution. Authors: Julia Smirnova / Justus Loerke / Gunnar Kleinau / Andrea Schmidt / Jörg Bürger / Etienne H Meyer / Thorsten Mielke / Patrick Scheerer / Ralph Bock / Christian M T Spahn / Reimo Zoschke / Abstract: In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are ...In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing.
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