- 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
cellular response to abscisic acid stimulus / adaxial/abaxial pattern specification / leaf morphogenesis / positive regulation of signal transduction / seed germination / response to high light intensity / MAP kinase scaffold activity / response to UV-B / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...cellular response to abscisic acid stimulus / adaxial/abaxial pattern specification / leaf morphogenesis / positive regulation of signal transduction / seed germination / response to high light intensity / MAP kinase scaffold activity / response to UV-B / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of LSU-rRNA / protein-RNA complex assembly / 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) / translation regulator activity / protein kinase C binding / rescue of stalled cytosolic ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / cytosolic ribosome / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / protein ubiquitination / rRNA binding / ribosome / translation / structural constituent of ribosome / ribonucleoprotein complex / cell division / mRNA binding / nucleolus / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol Similarity search - Function
Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / : ...Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Plectin/S10 domain / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / S27a-like superfamily / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal L40e family / Ribosomal protein L36e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal protein L35Ae, conserved site / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L35Ae signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ribosomal protein L44e / : / Ribosomal protein L44 / Ribosomal protein S7e signature. / Ribosomal protein 60S L18 and 50S L18e / 60S ribosomal protein L35 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L6e / Ribosomal protein L7A/L8 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site Similarity search - Domain/homology
40S ribosomal protein S25 / 60S ribosomal protein L35-like / Large ribosomal subunit protein eL30 / Ubiquitin-ribosomal protein eL40 fusion protein / Ribosomal protein L19 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein uS11y / 60S ribosomal protein L11-1 / Small ribosomal subunit protein uS5 ...40S ribosomal protein S25 / 60S ribosomal protein L35-like / Large ribosomal subunit protein eL30 / Ubiquitin-ribosomal protein eL40 fusion protein / Ribosomal protein L19 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein uS11y / 60S ribosomal protein L11-1 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL21z/eL21y-like / Large ribosomal subunit protein uL18-like / 40S ribosomal protein S30 / Small ribosomal subunit protein uS10y / 40S ribosomal protein S27 / 60S ribosomal protein L23 / Large ribosomal subunit protein eL33y / Large ribosomal subunit protein uL2-like / Large ribosomal subunit protein eL31 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S19-3 / Small ribosomal subunit protein uS13z/uS13y/uS13x / 60S ribosomal protein L29 / 60S ribosomal protein L39-3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL32z / 40S ribosomal protein S6 / 40S ribosomal protein S7 / Small ribosomal subunit protein eS17-like / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS15 / 40S ribosomal protein S24 / 40S ribosomal protein S21 / Large ribosomal subunit protein uL30y / Large ribosomal subunit protein eL14z / Small ribosomal subunit protein RACK1-like / 60S ribosomal protein L27 / 40S ribosomal protein S28 / Small ribosomal subunit protein uS9 / 60S ribosomal protein L44 / Large ribosomal subunit protein eL6 / 40S ribosomal protein S12 / Small ribosomal subunit protein uS4y / Large ribosomal subunit protein uL15x-like / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS3x / Large ribosomal subunit protein uL6z/uL6y / Ubiquitin-ribosomal protein eS31 fusion protein / 60S ribosomal protein L38 / 40S ribosomal protein S23 / Large ribosomal subunit protein uL22z / 60S ribosomal protein L18a / 60S ribosomal protein L13 / 40S ribosomal protein S26 / 40S ribosomal protein S8 / Large ribosomal subunit protein eL28z / 60S ribosomal protein L36 / Ribosomal protein L15 / 60S ribosomal protein L7a / Small ribosomal subunit protein uS8c / 60S ribosomal protein L18-2 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS10z / Large ribosomal subunit protein uL13w / Ribosomal protein L37 / Large ribosomal subunit protein uL24z / 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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