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- EMDB-35637: Wheat 80S ribosome stalled on AUG-Stop boron dependently with cyc... -
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Open data
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Basic information
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Title | Wheat 80S ribosome stalled on AUG-Stop boron dependently with cycloheximide | |||||||||
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![]() | ribosome / TRANSLATION | |||||||||
Function / homology | ![]() translation release factor complex / cytoplasmic translational termination / translation release factor activity, codon specific / sequence-specific mRNA binding / 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 / rescue of stalled ribosome ...translation release factor complex / cytoplasmic translational termination / translation release factor activity, codon specific / sequence-specific mRNA binding / 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 / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / 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 / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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 | ![]() | 228.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 99.7 KB 99.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 133.5 KB | ||
Filedesc metadata | ![]() | 19.9 KB | ||
Others | ![]() ![]() | 193.9 MB 193.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ipaMC ![]() 8ip8C ![]() 8ip9C ![]() 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: 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_35637_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35637_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Wheat 80S ribosome stalled on AUG-Stop boron dependently with cyc...
+Supramolecule #1: Wheat 80S ribosome stalled on AUG-Stop boron dependently with cyc...
+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 #80: 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 #79: eukaryotic release factor 1
+Macromolecule #81: MAGNESIUM ION
+Macromolecule #82: ZINC ION
+Macromolecule #83: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
-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: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
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 |