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- EMDB-14001: Specific features and methylation sites of a plant ribosome. 60S ... -
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Open data
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Basic information
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Title | Specific features and methylation sites of a plant ribosome. 60S ribosomal subunit. | |||||||||||||||
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Function / homology | ![]() protein-RNA complex assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
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Method | ![]() ![]() | |||||||||||||||
![]() | Cottilli P / Itoh Y / Amunts A | |||||||||||||||
Funding support | European Union, 4 items
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![]() | ![]() Title: Cryo-EM structure and rRNA modification sites of a plant ribosome. Authors: Patrick Cottilli / Yuzuru Itoh / Yuko Nobe / Anton S Petrov / Purificación Lisón / Masato Taoka / Alexey Amunts / ![]() ![]() ![]() ![]() Abstract: Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to ...Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology. | |||||||||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 331.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 64.2 KB 64.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19 KB | Display | ![]() |
Images | ![]() | 91 KB | ||
Masks | ![]() | 600.7 MB | ![]() | |
Filedesc metadata | ![]() | 13.9 KB | ||
Others | ![]() ![]() | 483.9 MB 483.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qiwMC ![]() 7qixC ![]() 7qiyC ![]() 7qizC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Sample components
+Entire : 60S ribosomal subunit
+Supramolecule #1: 60S ribosomal subunit
+Macromolecule #1: 60S ribosomal protein L8
+Macromolecule #2: Ribos_L4_asso_C domain-containing protein
+Macromolecule #3: Ribosomal protein L3
+Macromolecule #4: Ribosomal_L18_c domain-containing protein
+Macromolecule #5: Ribosomal_L6e_N domain-containing protein
+Macromolecule #6: Thaliana 60S ribosomal protein L7
+Macromolecule #7: Ribosomal_L7Ae domain-containing protein
+Macromolecule #8: 60S ribosomal protein uL6
+Macromolecule #9: 60S ribosomal protein L10
+Macromolecule #10: 60S ribosomal protein uL5
+Macromolecule #11: 60S ribosomal protein L13
+Macromolecule #12: Ribosomal_L14e domain-containing protein
+Macromolecule #13: Ribosomal protein L15
+Macromolecule #14: 60S ribosomal protein uL13
+Macromolecule #15: 50S ribosomal protein L22, chloroplastic
+Macromolecule #16: Ribosomal_L18e/L15P domain-containing protein
+Macromolecule #17: Ribosomal protein L19
+Macromolecule #18: 60S ribosomal protein L18a
+Macromolecule #19: 60S ribosomal protein eL21
+Macromolecule #20: 60S ribosomal protein eL22
+Macromolecule #21: 60S ribosomal protein uL14
+Macromolecule #22: TRASH domain-containing protein
+Macromolecule #23: Ribosomal_L23eN domain-containing protein
+Macromolecule #24: KOW domain-containing protein
+Macromolecule #25: 60S ribosomal protein L27
+Macromolecule #26: Putative 60S ribosomal protein L27a-3-like
+Macromolecule #27: 60S ribosomal protein L29
+Macromolecule #28: Ribosomal_L7Ae domain-containing protein
+Macromolecule #29: 60S ribosomal protein eL31
+Macromolecule #30: 60S ribosomal protein eL32
+Macromolecule #31: 60S ribosomal protein eL33
+Macromolecule #32: 60S ribosomal protein eL34
+Macromolecule #33: Similar to 60S ribosomal protein L35
+Macromolecule #34: 60S ribosomal protein L36
+Macromolecule #35: Ribosomal protein L37
+Macromolecule #36: 60S ribosomal protein L38
+Macromolecule #37: 60S ribosomal protein eL39
+Macromolecule #38: Ubiquitin-like domain-containing protein
+Macromolecule #39: 60S ribosomal protein eL42
+Macromolecule #40: 60S ribosomal protein eL43
+Macromolecule #41: Ribosomal_L28e domain-containing protein
+Macromolecule #42: tRNA
+Macromolecule #43: 25S rRNA
+Macromolecule #44: 5S rRNA
+Macromolecule #45: 5.8S rRNA
+Macromolecule #46: POTASSIUM ION
+Macromolecule #47: MAGNESIUM ION
+Macromolecule #48: ZINC ION
+Macromolecule #49: SPERMINE
+Macromolecule #50: SPERMIDINE
+Macromolecule #51: water
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.2 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |