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Yorodumi- EMDB-51820: Structure of the Arabidopsis thaliana 80S ribosome in complex wit... -
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Open data
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Basic information
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| Title | Structure of the Arabidopsis thaliana 80S ribosome in complex with P- and E-site tRNAs and mRNA | ||||||||||||
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Keywords | plant / thermospermine / methylation / rRNA modification / RIBOSOME | ||||||||||||
| Function / homology | Function and homology informationroot morphogenesis / trichome morphogenesis / cytokinesis by cell plate formation / adaxial/abaxial pattern specification / leaf morphogenesis / response to high light intensity / plant-type cell wall / developmental process / chloroplast envelope / plasmodesma ...root morphogenesis / trichome morphogenesis / cytokinesis by cell plate formation / adaxial/abaxial pattern specification / leaf morphogenesis / response to high light intensity / plant-type cell wall / developmental process / chloroplast envelope / plasmodesma / plant-type vacuole / vacuole / response to UV-B / response to osmotic stress / nucleocytoplasmic transport / plastid / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / maturation of LSU-rRNA / response to salt stress / 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) / cytosolic ribosome / response to cold / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / small-subunit processome / modification-dependent protein catabolic process / protein tag activity / rRNA processing / peroxisome / ribosome biogenesis / ribosomal small subunit assembly / ribosomal small subunit biogenesis / response to oxidative stress / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / defense response to bacterium / rRNA binding / structural constituent of ribosome / protein ubiquitination / ribosome / translation / ribonucleoprotein complex / cell division / mRNA binding / ubiquitin protein ligase binding / nucleolus / endoplasmic reticulum / mitochondrion / RNA binding / extracellular region / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
| Biological species | ![]() | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 1.82 Å | ||||||||||||
Authors | Faille A / Warren AJ | ||||||||||||
| Funding support | United Kingdom, European Union, 3 items
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Citation | Journal: Science / Year: 2026Title: Structure of the Arabidopsis thaliana 80S ribosome in complex with P- and E-site tRNAs and mRNA Authors: Faille A / Warren AJ / Hellmann E / Ko D / Ruonala R / Helariutta YE | ||||||||||||
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_51820.map.gz | 1.1 GB | EMDB map data format | |
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| Header (meta data) | emd-51820-v30.xml emd-51820.xml | 101.4 KB 101.4 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_51820_fsc.xml | 22.5 KB | Display | FSC data file |
| Images | emd_51820.png | 165.3 KB | ||
| Filedesc metadata | emd-51820.cif.gz | 20.2 KB | ||
| Others | emd_51820_half_map_1.map.gz emd_51820_half_map_2.map.gz | 1.1 GB 1.1 GB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-51820 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-51820 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9h3gMC ![]() 9h6iC ![]() 9hesC ![]() 9hmwC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_51820.map.gz / Format: CCP4 / Size: 1.2 GB / 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: 0.723 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_51820_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_51820_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Ribosome in complex with P- and E-site tRNAs, mRNA, and polypeptide
+Supramolecule #1: Ribosome in complex with P- and E-site tRNAs, mRNA, and polypeptide
+Macromolecule #1: Ribosomal RNA 5.8S
+Macromolecule #2: Ribosomal RNA 25S
+Macromolecule #3: Transfer RNA Phe
+Macromolecule #4: Ribosomal RNA 5S
+Macromolecule #75: Ribosomal RNA 18S
+Macromolecule #76: Messenger RNA (poly-U)
+Macromolecule #5: Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v
+Macromolecule #6: Large ribosomal subunit protein uL22z
+Macromolecule #7: Large ribosomal subunit protein uL24z
+Macromolecule #8: 60S ribosomal protein L29
+Macromolecule #9: Large ribosomal subunit protein eL31y
+Macromolecule #10: Small ribosomal subunit protein eS26y
+Macromolecule #11: Large ribosomal subunit protein uL6z/uL6y
+Macromolecule #12: Small ribosomal subunit protein uS8z/uS8w
+Macromolecule #13: Large ribosomal subunit protein eL36y
+Macromolecule #14: Large ribosomal subunit protein eL27x
+Macromolecule #15: Small ribosomal subunit protein eS4x
+Macromolecule #16: Large ribosomal subunit protein eL15z
+Macromolecule #17: Ribosomal protein L18ae/LX family protein
+Macromolecule #18: Small ribosomal subunit protein uS12y
+Macromolecule #19: Small ribosomal subunit protein eS24y
+Macromolecule #20: Large ribosomal subunit protein eL33y
+Macromolecule #21: Large ribosomal subunit protein eL42z/eL42y
+Macromolecule #22: Large ribosomal subunit protein uL3z
+Macromolecule #23: Large ribosomal subunit protein eL21z/eL21y
+Macromolecule #24: Small ribosomal subunit protein uS5y/uS5u/uS5v
+Macromolecule #25: Large ribosomal subunit protein uL14x/uL14z/uL14y
+Macromolecule #26: Large ribosomal subunit protein eL14y
+Macromolecule #27: Large ribosomal subunit protein uL4z
+Macromolecule #28: Large ribosomal subunit protein eL32z
+Macromolecule #29: Small ribosomal subunit protein uS7y
+Macromolecule #30: Large ribosomal subunit protein eL18x
+Macromolecule #31: Large ribosomal subunit protein uL2z
+Macromolecule #32: Large ribosomal subunit protein uL13y
+Macromolecule #33: Small ribosomal subunit protein uS15y
+Macromolecule #34: Large ribosomal subunit protein uL18z
+Macromolecule #35: Large ribosomal subunit protein eL30y
+Macromolecule #36: Small ribosomal subunit protein eS30z/eS30y/eS30x
+Macromolecule #37: Large ribosomal subunit protein uL29x
+Macromolecule #38: Large ribosomal subunit protein uL23y
+Macromolecule #39: Large ribosomal subunit protein eL8y
+Macromolecule #40: Large ribosomal subunit protein eL34z
+Macromolecule #41: Large ribosomal subunit protein uL15x
+Macromolecule #42: Large ribosomal subunit protein uL5z
+Macromolecule #43: Ribosomal protein L30/L7 family protein
+Macromolecule #44: Small ribosomal subunit protein uS17z
+Macromolecule #45: Small ribosomal subunit protein eS1y
+Macromolecule #46: Large ribosomal subunit protein uL16y
+Macromolecule #47: Large ribosomal subunit protein eL24z
+Macromolecule #48: Small ribosomal subunit protein eS21y
+Macromolecule #49: Large ribosomal subunit protein eL19x
+Macromolecule #50: Small ribosomal subunit protein eS27y
+Macromolecule #51: Small ribosomal subunit protein uS4y
+Macromolecule #52: Large ribosomal subunit protein eL6y
+Macromolecule #53: Small ribosomal subunit protein uS3z
+Macromolecule #54: Large ribosomal subunit protein eL13z
+Macromolecule #55: Ubiquitin-ribosomal protein eL40z fusion protein
+Macromolecule #56: Large ribosomal subunit protein eL39z/eL39x
+Macromolecule #57: Small ribosomal subunit protein uS9z
+Macromolecule #58: Small ribosomal subunit protein uS13z/uS13y/uS13x
+Macromolecule #59: Small ribosomal subunit protein eS6y
+Macromolecule #60: Large ribosomal subunit protein eL38z/eL38y
+Macromolecule #61: Large ribosomal subunit protein eL43y
+Macromolecule #62: Small ribosomal subunit protein uS2z
+Macromolecule #63: Large ribosomal subunit protein eL28z
+Macromolecule #64: Small ribosomal subunit protein eS28x
+Macromolecule #65: Small ribosomal subunit protein uS11y
+Macromolecule #66: Small ribosomal subunit protein uS19y
+Macromolecule #67: Small ribosomal subunit protein eS17w
+Macromolecule #68: Large ribosomal subunit protein eL22z
+Macromolecule #69: Small ribosomal subunit protein eS7x
+Macromolecule #70: Small ribosomal subunit protein eS19x
+Macromolecule #71: Small ribosomal subunit protein eS25w
+Macromolecule #72: Small ribosomal subunit protein eS8z
+Macromolecule #73: Large ribosomal subunit protein eL37z
+Macromolecule #74: Small ribosomal subunit protein uS14z/uS14y/uS14x
+Macromolecule #77: Small ribosomal subunit protein uS10y
+Macromolecule #78: Small ribosomal subunit protein eS10z
+Macromolecule #79: Nascent polypeptide (poly-A)
+Macromolecule #80: MAGNESIUM ION
+Macromolecule #81: POTASSIUM ION
+Macromolecule #82: N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE
+Macromolecule #83: SPERMIDINE
+Macromolecule #84: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
+Macromolecule #85: ZINC ION
+Macromolecule #86: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| 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 | TFS KRIOS |
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| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Keywords
Authors
United Kingdom, European Union, 3 items
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Processing
FIELD EMISSION GUN

