+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15674 | |||||||||
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Title | Cryo-EM structure of the plant 40S subunit | |||||||||
Map data | The small subunit (40S) of the tobacco ribosome from cytosol | |||||||||
Sample |
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Keywords | Plant / 80S / 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) / 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) / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / maintenance of translational fidelity ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Nicotiana tabacum (common tobacco) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.38 Å | |||||||||
Authors | Smirnova J / Loerke J / Kleinau G / Schmidt A / Buerger J / Meyer EH / Mielke T / Scheerer P / Bock R / Spahn CMT / Zoschke R | |||||||||
Funding support | Germany, 2 items
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Citation | 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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15674.map.gz | 14.8 MB | EMDB map data format | |
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Header (meta data) | emd-15674-v30.xml emd-15674.xml | 52.4 KB 52.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15674_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_15674.png | 101.5 KB | ||
Masks | emd_15674_msk_1.map | 347.6 MB | Mask map | |
Filedesc metadata | emd-15674.cif.gz | 12 KB | ||
Others | emd_15674_half_map_1.map.gz emd_15674_half_map_2.map.gz | 323 MB 323.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15674 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15674 | HTTPS FTP |
-Validation report
Summary document | emd_15674_validation.pdf.gz | 945.1 KB | Display | EMDB validaton report |
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Full document | emd_15674_full_validation.pdf.gz | 944.6 KB | Display | |
Data in XML | emd_15674_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | emd_15674_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15674 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15674 | HTTPS FTP |
-Related structure data
Related structure data | 8auvMC 8azwC 8b2lC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15674.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | The small subunit (40S) of the tobacco ribosome from cytosol | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.848 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15674_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half-map A of the tobacco ribosome after local refinement...
File | emd_15674_half_map_1.map | ||||||||||||
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Annotation | Half-map_A of the tobacco ribosome after local refinement of the small subunit (40S) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map B of the tobacco ribosome after local refinement...
File | emd_15674_half_map_2.map | ||||||||||||
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Annotation | Half-map_B of the tobacco ribosome after local refinement of the small subunit (40S) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 40S subunit of the cytosolic 80S ribosome from tobacco
+Supramolecule #1: 40S subunit of the cytosolic 80S ribosome from tobacco
+Macromolecule #1: eS4 (40S ribosomal protein S4)
+Macromolecule #2: eS6 (40S ribosomal protein S6)
+Macromolecule #4: eS10 (40S ribosomal protein S10)
+Macromolecule #5: eS12 (40S ribosomal protein S12)
+Macromolecule #6: eS17 (40S ribosomal protein S17)
+Macromolecule #7: eS19 (40S ribosomal protein S19)
+Macromolecule #8: eS1 (40S ribosomal protein S3a)
+Macromolecule #9: eS21 (40S ribosomal protein S21)
+Macromolecule #10: eS24 (40S ribosomal protein S24)
+Macromolecule #11: eS25 (40S ribosomal protein S25)
+Macromolecule #12: eS26 (40S ribosomal protein S26)
+Macromolecule #13: eS27 (40S ribosomal protein S27)
+Macromolecule #14: eS28 (40S ribosomal protein S28)
+Macromolecule #15: eS30 (40S ribosomal protein S30)
+Macromolecule #16: eS31 (ubiquitin-40S ribosomal protein S27a)
+Macromolecule #17: eS7 (40S ribosomal protein S7)
+Macromolecule #18: eS8 (40S ribosomal protein S8)
+Macromolecule #19: RACK1 (guanine nucleotide-binding protein subunit beta-like protein)
+Macromolecule #20: uS10 (40S ribosomal protein S20)
+Macromolecule #21: uS11 (40S ribosomal protein S14)
+Macromolecule #22: uS12 (40S ribosomal protein S23)
+Macromolecule #23: uS13 (40S ribosomal protein S18)
+Macromolecule #24: uS14 (40S ribosomal protein S29)
+Macromolecule #25: uS15 (40S ribosomal protein S13)
+Macromolecule #26: uS17 (40S ribosomal protein S11)
+Macromolecule #27: uS19 (40S ribosomal protein S15)
+Macromolecule #28: uS2 (40S ribosomal protein SA)
+Macromolecule #29: uS3 (40S ribosomal protein S3)
+Macromolecule #30: uS4 (40S ribosomal protein S9)
+Macromolecule #31: uS5 (40S ribosomal protein S2)
+Macromolecule #32: uS7 (40S ribosomal protein S5)
+Macromolecule #33: uS8 (40S ribosomal protein S15a)
+Macromolecule #34: uS9 (40S ribosomal protein S16)
+Macromolecule #3: 18S rRNA
+Macromolecule #35: mRNA
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: POTASSIUM ION
+Macromolecule #38: SPERMIDINE
+Macromolecule #39: SPERMINE
+Macromolecule #40: ZINC ION
+Macromolecule #41: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 27.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |