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Open data
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Basic information
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Title | Wheat 40S ribosome in complex with a tRNAi | |||||||||
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![]() | ribosome / TRANSLATION | |||||||||
Function / homology | ![]() 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 / rRNA processing ...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 / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / ribosome binding / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Yokoyama T / Tanaka M / Saito H / Nishimoto M / Tsuda K / Sotta N / Shigematsu H / Shirouzu M / Iwasaki S / Ito T / Fujiwara T | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Authors: Mayuki Tanaka / Takeshi Yokoyama / Hironori Saito / Madoka Nishimoto / Kengo Tsuda / Naoyuki Sotta / Hideki Shigematsu / Mikako Shirouzu / Shintaro Iwasaki / Takuhiro Ito / Toru Fujiwara / ![]() Abstract: In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is ...In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is downregulated in response to an excess amount of boric acid in the environment through upstream open reading frames (uORFs) that consist of only AUG and stop codons. However, the molecular details of how this minimum uORF controls translation of the downstream main ORF in a boric acid-dependent manner have remained unclear. Here, by combining ribosome profiling, translation complex profile sequencing, structural analysis with cryo-electron microscopy and biochemical assays, we show that the 80S ribosome assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 on the 80S ribosome on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 627.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 50.6 KB 50.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.8 KB | Display | ![]() |
Images | ![]() | 113 KB | ||
Filedesc metadata | ![]() | 11.3 KB | ||
Others | ![]() ![]() | 540.6 MB 540.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ip9MC ![]() 8ip8C ![]() 8ipaC ![]() 8ipbC 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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Voxel size | X=Y=Z: 0.788 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35635_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35635_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Wheat 40S ribosome in complex with a tRNAi
+Supramolecule #1: Wheat 40S ribosome in complex with a tRNAi
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #34: mRNA
+Macromolecule #35: tRNAi
+Macromolecule #2: 40S ribosomal protein eS24
+Macromolecule #3: 40S ribosomal protein eS8
+Macromolecule #4: 40S ribosomal protein eS10
+Macromolecule #5: 40S ribosomal protein S23
+Macromolecule #6: RACK1
+Macromolecule #7: 40S ribosomal protein uS3
+Macromolecule #8: 40S ribosomal protein eS4
+Macromolecule #9: 40S ribosomal protein uS7
+Macromolecule #10: 40S ribosomal protein uS9
+Macromolecule #11: 40S ribosomal protein uS10
+Macromolecule #12: 40S ribosomal protein uS11
+Macromolecule #13: 40S ribosomal protein uS13
+Macromolecule #14: 40S ribosomal protein uS15
+Macromolecule #15: 40S ribosomal protein eS17
+Macromolecule #16: 40S ribosomal protein eS19
+Macromolecule #17: 40S ribosomal protein uS19
+Macromolecule #18: 40S ribosomal protein eS25
+Macromolecule #19: 40S ribosomal protein eS28
+Macromolecule #20: 40S ribosomal protein uS8
+Macromolecule #21: 40S ribosomal protein uS14
+Macromolecule #22: 40S ribosomal protein eS27
+Macromolecule #23: 40S ribosomal protein eS30
+Macromolecule #24: 40S ribosomal protein uS2
+Macromolecule #25: 40S ribosomal protein eS1
+Macromolecule #26: 40S ribosomal protein eS21
+Macromolecule #27: 40S ribosomal protein eS26
+Macromolecule #28: 40S ribosomal protein uS4
+Macromolecule #29: 40S ribosomal protein uS5
+Macromolecule #30: 40S ribosomal protein eS6
+Macromolecule #31: 40S ribosomal protein eS7
+Macromolecule #32: 40S ribosomal protein uS17
+Macromolecule #33: 60S ribosomal protein eL41
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |