- EMDB-15806: Cryo-EM structure of the plant 80S ribosome -
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Basic information
Entry
Database: EMDB / ID: EMD-15806
Title
Cryo-EM structure of the plant 80S ribosome
Map data
Tobacco 80S ribosome from cytosol
Sample
Complex: 40S subunit of the cytosolic 80S ribosome from tobacco
Protein or peptide: x 76 types
RNA: x 6 types
Ligand: x 6 types
Keywords
Plant / 80S / rRNA Modifications / ribosome
Function / homology
Function and homology information
endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm 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 S26e signature. / : / Ribosomal protein L41 ...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 S26e signature. / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / metallochaperone-like domain / Ribosomal protein S12e signature. / TRASH domain / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / : / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L44e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L10e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S3, eukaryotic/archaeal / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein S4e signature. / Ribosomal protein L34e, conserved site / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e Similarity search - Domain/homology
40S ribosomal protein S25 / 60S ribosomal protein L35-like / 60S ribosomal protein L30-like / Ubiquitin-60S ribosomal protein L40 / Ribosomal protein L19 / 60S ribosomal protein L4-like / 60S ribosomal protein L37a / 40S ribosomal protein S14-2 / 60S ribosomal protein L11-1 / 40S ribosomal protein S2-3-like ...40S ribosomal protein S25 / 60S ribosomal protein L35-like / 60S ribosomal protein L30-like / Ubiquitin-60S ribosomal protein L40 / Ribosomal protein L19 / 60S ribosomal protein L4-like / 60S ribosomal protein L37a / 40S ribosomal protein S14-2 / 60S ribosomal protein L11-1 / 40S ribosomal protein S2-3-like / 60S ribosomal protein L21-1-like / 60S ribosomal protein L5-like / 40S ribosomal protein S30 / 40S ribosomal protein S20-2 / 40S ribosomal protein S27 / 60S ribosomal protein L23 / 60S ribosomal protein L35a-3 / 60S ribosomal protein L8-like / 60S ribosomal protein L31 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S19-3 / 40S ribosomal protein S18 / 60S ribosomal protein L29 / 60S ribosomal protein L39-3 / 60S ribosomal protein L10-like / 60S ribosomal protein L32-1 / 40S ribosomal protein S6 / 40S ribosomal protein S7 / 40S ribosomal protein S17-like / 60S ribosomal protein L3 / 40S ribosomal protein S13 / 40S ribosomal protein S24 / 40S ribosomal protein S21 / 60S ribosomal protein L7-4-like / 60S ribosomal protein L14-1 / Guanine nucleotide-binding protein subunit beta-like protein / 60S ribosomal protein L27 / 40S ribosomal protein S28 / 40S ribosomal protein S16 / 60S ribosomal protein L44 / 60S ribosomal protein L6-like isoform X1 / 40S ribosomal protein S12 / 40S ribosomal protein S9-2-like / 60S ribosomal protein L27a-3-like / 60S ribosomal protein L24-like / 60S ribosomal protein L22-2-like / 40S ribosomal protein S11-like / 40S ribosomal protein S5-like / 40S ribosomal protein S3-2-like / 60S ribosomal protein L9-1-like / Ubiquitin-40S ribosomal protein S27a-like / 60S ribosomal protein L38 / 40S ribosomal protein S23 / 60S ribosomal protein L17-1-like / 60S ribosomal protein L18a / 60S ribosomal protein L13 / 40S ribosomal protein S26 / 40S ribosomal protein S8 / 60S ribosomal protein L28-1-like / 60S ribosomal protein L36 / Ribosomal protein L15 / 60S ribosomal protein L7a / 40S ribosomal protein S15a-1 / 60S ribosomal protein L18-2-like / 40S ribosomal protein S15-like / 40S ribosomal protein S10-1-like / 60S ribosomal protein L13a-4 / Ribosomal protein L37 / 60S ribosomal protein L26-1-like / 40S ribosomal protein S29 / 40S ribosomal protein S4 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS1 Similarity search - Component
Biological species
Nicotiana tabacum (common tobacco)
Method
single particle reconstruction / cryo EM / Resolution: 2.2 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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