+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35638 | |||||||||
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Title | Wheat 80S ribosome pausing on AUG-Stop with cycloheximide | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ribosome / TRANSLATION | |||||||||
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 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / 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 / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Triticum aestivum (bread wheat) / Oryza sativa (Asian cultivated rice) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Yokoyama T / Tanaka M / Saito H / Nishimoto M / Tsuda K / Sotta N / Shigematsu H / Shirouzu M / Iwasaki S / Ito T / Fujiwara T | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: Nat Chem Biol / Year: 2024 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 | emd_35638.map.gz | 229.1 MB | EMDB map data format | |
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Header (meta data) | emd-35638-v30.xml emd-35638.xml | 98.2 KB 98.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35638_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_35638.png | 136.3 KB | ||
Filedesc metadata | emd-35638.cif.gz | 19.4 KB | ||
Others | emd_35638_half_map_1.map.gz emd_35638_half_map_2.map.gz | 193.9 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35638 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35638 | HTTPS FTP |
-Validation report
Summary document | emd_35638_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_35638_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_35638_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | emd_35638_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35638 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35638 | HTTPS FTP |
-Related structure data
Related structure data | 8ipbMC 8ip8C 8ip9C 8ipaC 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_35638.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.47 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35638_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35638_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Wheat 80S ribosome pausing on AUG-Stop with cycloheximide
+Supramolecule #1: Wheat 80S ribosome pausing on AUG-Stop with cycloheximide
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #75: 60S ribosomal RNA
+Macromolecule #76: 5.8S ribosomal RNA
+Macromolecule #77: 5S ribosomal RNA
+Macromolecule #78: mRNA
+Macromolecule #79: tRNAi
+Macromolecule #2: 40S ribosomal protein eS24
+Macromolecule #3: 40S ribosomal protein eS8
+Macromolecule #4: 40S ribosomal protein eS10
+Macromolecule #5: 40S ribosomal protein uS12
+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: 40S ribosomal protein eL8
+Macromolecule #34: 60S ribosomal protein eL21
+Macromolecule #35: 60S ribosomal protein eL27
+Macromolecule #36: 60S ribosomal protein uL2
+Macromolecule #37: 60S ribosomal protein uL5
+Macromolecule #38: 60S ribosomal protein uL6
+Macromolecule #39: 60S ribosomal protein uL14
+Macromolecule #40: 60S ribosomal protein eL15
+Macromolecule #41: 60S ribosomal protein uL15
+Macromolecule #42: 60S ribosomal protein eL18
+Macromolecule #43: 60S ribosomal protein uL18
+Macromolecule #44: 60S ribosomal protein eL19
+Macromolecule #45: 60S ribosomal protein uL22
+Macromolecule #46: 60S ribosomal protein uL23
+Macromolecule #47: 60S ribosomal protein eL24
+Macromolecule #48: 60S ribosomal protein uL24
+Macromolecule #49: 60S ribosomal protein eL28
+Macromolecule #50: 60S ribosomal protein eL30
+Macromolecule #51: 60S ribosomal protein eL31
+Macromolecule #52: 60S ribosomal protein eL32
+Macromolecule #53: 60S ribosomal protein eL37
+Macromolecule #54: 60S ribosomal protein eL39
+Macromolecule #55: 60S ribosomal protein eL42
+Macromolecule #56: 60S ribosomal protein eL14
+Macromolecule #57: 60S ribosomal protein eL20
+Macromolecule #58: 60S ribosomal protein eL22
+Macromolecule #59: 60S ribosomal protein eL36
+Macromolecule #60: 60S ribosomal protein uL29
+Macromolecule #61: 60S ribosomal protein uL30
+Macromolecule #62: 60S ribosomal protein uL3
+Macromolecule #63: 60S ribosomal protein uL4
+Macromolecule #64: 60S ribosomal protein uL13
+Macromolecule #65: 60S ribosomal protein eL43
+Macromolecule #66: 60S ribosomal protein uL16
+Macromolecule #67: 60S ribosomal protein eL41
+Macromolecule #68: 60S ribosomal protein eL40
+Macromolecule #69: 60S ribosomal protein eL13
+Macromolecule #70: 60S ribosomal protein eL6
+Macromolecule #71: 60S ribosomal protein eL33
+Macromolecule #72: 60S ribosomal protein eL38
+Macromolecule #73: 60S ribosomal protein eL29
+Macromolecule #74: 60S ribosomal protein eL34
+Macromolecule #80: MAGNESIUM ION
+Macromolecule #81: ZINC ION
+Macromolecule #82: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 23500 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |