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Open data
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Basic information
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| Title | WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU) | |||||||||
Map data | Combined post-processed maps of the 60S and 40S subunits were obtained from multibody refinement in RELION. The resulting maps were aligned to the consensus 3D refinement map after polishing | |||||||||
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Keywords | 80S Ribosome / TISU mRNA / Human / eS26 / WT-HEK / RIBOSOME | |||||||||
| Function / homology | Function and homology informationembryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex ...embryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / axial mesoderm development / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of ubiquitin-protein transferase activity / positive regulation of respiratory burst involved in inflammatory response / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / positive regulation of DNA-templated transcription initiation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / nucleolus organization / TNFR1-mediated ceramide production / alpha-beta T cell differentiation / positive regulation of DNA damage response, signal transduction by p53 class mediator / GAIT complex / negative regulation of RNA splicing / TORC2 complex binding / neural crest cell differentiation / supercoiled DNA binding / cytoplasmic translational initiation / NF-kappaB complex / negative regulation of DNA repair / G1 to G0 transition / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / rRNA modification in the nucleus and cytosol / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / ion channel inhibitor activity / protein kinase A binding / laminin receptor activity / Ribosomal scanning and start codon recognition / pigmentation / homeostatic process / positive regulation of mitochondrial depolarization / Translation initiation complex formation / macrophage chemotaxis / lung morphogenesis / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / fibroblast growth factor binding / Protein hydroxylation / monocyte chemotaxis / BH3 domain binding / negative regulation of translational frameshifting / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / SARS-CoV-1 modulates host translation machinery / positive regulation of GTPase activity / TOR signaling / mTORC1-mediated signalling / iron-sulfur cluster binding / Peptide chain elongation / regulation of cell division / cellular response to ethanol / Selenocysteine synthesis / Formation of a pool of free 40S subunits / negative regulation of protein binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Eukaryotic Translation Termination / protein serine/threonine kinase inhibitor activity / blastocyst development / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / negative regulation of respiratory burst involved in inflammatory response / Viral mRNA Translation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / negative regulation of ubiquitin-dependent protein catabolic process / protein localization to nucleus / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / protein targeting Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Hiregange DG / Fraticelli D / Bashan A / Yonath A / Dikstein R | |||||||||
| Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2026Title: Structural and molecular basis of specialized translation mediated by the ribosome mRNA-binding channel. Authors: Davide Fraticelli / Disha Gajanan Hiregange / Benjamin Weiss / Ariel Ogran / Tal Havkin-Solomon / Irene Martinez Roman / Anat Bashan / Ada Yonath / Rivka Dikstein / ![]() Abstract: The ribosome mRNA channel is central to translation, yet its role in regulatory mechanisms remains unclear. Using cryo-EM of human ribosomal complexes bound to Kozak and TISU mRNAs from wild-type (WT) ...The ribosome mRNA channel is central to translation, yet its role in regulatory mechanisms remains unclear. Using cryo-EM of human ribosomal complexes bound to Kozak and TISU mRNAs from wild-type (WT) and RPS26/eS26 mutant (RPS26dC) cells, we demonstrate that both RPS26/eS26 and mRNA adopt distinct conformations, explaining the opposing effects of RPS26dC on their activity. Translatome studies of WT and RPS26dC reveal AUG-context-dependent changes in 48S and 80S initiation complexes and slower scanning. Downregulated mRNAs are enriched for specific AUG-upstream nucleotides and a -1-cytosine contacting 18S rRNA G1207, an interaction lost in RPS26dC. Strongly affected transcripts include replication-dependent histones, which, despite short 5'UTRs and suboptimal Kozak, exhibit robust translation activity that is RPS26/eS26-dependent. We identify a translational enhancer in the H2B 5'UTR (-16 to -9) overlapping predicted RPS26/eS26-binding sites, with a distinct ribosome-bound conformation. Exploiting these features, we engineered a high-efficiency translational cassette with minimal leaky scanning. These findings underscore the role of the ribosome's mRNA channel in selective translation and its therapeutic potential. | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_54266.map.gz | 57.7 MB | EMDB map data format | |
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| Header (meta data) | emd-54266-v30.xml emd-54266.xml | 103.5 KB 103.5 KB | Display Display | EMDB header |
| Images | emd_54266.png | 79.7 KB | ||
| Filedesc metadata | emd-54266.cif.gz | 21 KB | ||
| Others | emd_54266_additional_1.map.gz | 364 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-54266 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-54266 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9ru8MC ![]() 9ru7C ![]() 9ru9C ![]() 9ruaC ![]() 9rucC ![]() 55215 ![]() 55216 ![]() 55217 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_54266.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Combined post-processed maps of the 60S and 40S subunits were obtained from multibody refinement in RELION. The resulting maps were aligned to the consensus 3D refinement map after polishing | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.842 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: Combined non-postprocessed maps of the 60S and 40S...
| File | emd_54266_additional_1.map | ||||||||||||
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| Annotation | Combined non-postprocessed maps of the 60S and 40S subunits were obtained from multibody refinement in RELION. The resulting maps were aligned to the consensus 3D refinement map after polishing | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU)
+Supramolecule #1: WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU)
+Macromolecule #1: Ubiquitin-60S ribosomal protein L40
+Macromolecule #2: Large ribosomal subunit protein eL39
+Macromolecule #3: Large ribosomal subunit protein eL42
+Macromolecule #4: 40S ribosomal protein S24
+Macromolecule #5: Small ribosomal subunit protein uS12
+Macromolecule #6: 40S ribosomal protein S15a
+Macromolecule #7: 40S ribosomal protein S21
+Macromolecule #8: 40S ribosomal protein S17
+Macromolecule #9: 40S ribosomal protein S16
+Macromolecule #10: 40S ribosomal protein S14
+Macromolecule #11: 40S ribosomal protein S13
+Macromolecule #12: Small ribosomal subunit protein uS17
+Macromolecule #13: Small ribosomal subunit protein eS10
+Macromolecule #14: 40S ribosomal protein S9
+Macromolecule #15: 40S ribosomal protein S7
+Macromolecule #16: Small ribosomal subunit protein RACK1
+Macromolecule #17: Small ribosomal subunit protein uS7
+Macromolecule #18: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #19: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #20: 40S ribosomal protein S3
+Macromolecule #21: 40S ribosomal protein S29
+Macromolecule #22: 40S ribosomal protein S2
+Macromolecule #23: 40S ribosomal protein S28
+Macromolecule #24: 40S ribosomal protein S3a
+Macromolecule #25: 40S ribosomal protein S27
+Macromolecule #26: 40S ribosomal protein SA
+Macromolecule #27: 60S ribosomal protein L27
+Macromolecule #28: Large ribosomal subunit protein uL24
+Macromolecule #29: 60S ribosomal protein L23a
+Macromolecule #30: 60S ribosomal protein L24
+Macromolecule #31: 60S ribosomal protein L23
+Macromolecule #32: 60S ribosomal protein L22
+Macromolecule #33: 60S ribosomal protein L21
+Macromolecule #34: 60S ribosomal protein L18a
+Macromolecule #35: 60S ribosomal protein L19
+Macromolecule #36: Large ribosomal subunit protein eL28
+Macromolecule #37: 60S ribosomal protein L18
+Macromolecule #38: Large ribosomal subunit protein uL22
+Macromolecule #39: Large ribosomal subunit protein eL43
+Macromolecule #40: 60S ribosomal protein L13a
+Macromolecule #41: 60S ribosomal protein L15
+Macromolecule #42: Small ribosomal subunit protein eS32
+Macromolecule #43: 60S ribosomal protein L14
+Macromolecule #44: 60S ribosomal protein L13
+Macromolecule #45: 60S ribosomal protein L38
+Macromolecule #46: 60S ribosomal protein L11
+Macromolecule #47: Large ribosomal subunit protein eL37
+Macromolecule #48: 60S ribosomal protein L10
+Macromolecule #49: 60S ribosomal protein L36
+Macromolecule #50: 60S ribosomal protein L9
+Macromolecule #51: 60S ribosomal protein L35
+Macromolecule #52: 60S ribosomal protein L7a
+Macromolecule #53: Large ribosomal subunit protein eL34
+Macromolecule #54: Large ribosomal subunit protein uL30
+Macromolecule #55: Large ribosomal subunit protein eL33
+Macromolecule #56: Large ribosomal subunit protein eL6
+Macromolecule #57: 60S ribosomal protein L32
+Macromolecule #58: 60S ribosomal protein L5
+Macromolecule #59: 60S ribosomal protein L31
+Macromolecule #60: 60S ribosomal protein L4
+Macromolecule #61: 60S ribosomal protein L30
+Macromolecule #62: Large ribosomal subunit protein uL3
+Macromolecule #63: Large ribosomal subunit protein eL29
+Macromolecule #64: Large ribosomal subunit protein uL2
+Macromolecule #65: Large ribosomal subunit protein uL15
+Macromolecule #68: 40S ribosomal protein S26
+Macromolecule #71: Small ribosomal subunit protein eS25
+Macromolecule #72: 40S ribosomal protein S19
+Macromolecule #73: 40S ribosomal protein S15
+Macromolecule #75: 40S ribosomal protein S6
+Macromolecule #76: 40S ribosomal protein S8
+Macromolecule #78: Small ribosomal subunit protein uS13
+Macromolecule #80: 40S ribosomal protein S20
+Macromolecule #66: 5S rRNA
+Macromolecule #67: P site tRNA
+Macromolecule #69: 5.8S rRNA
+Macromolecule #70: 28S rRNA
+Macromolecule #74: 18S rRNA
+Macromolecule #77: E site tRNA
+Macromolecule #79: TISU mRNA
+Macromolecule #81: ZINC ION
+Macromolecule #82: POTASSIUM ION
+Macromolecule #83: MAGNESIUM ION
+Macromolecule #84: SODIUM ION
+Macromolecule #85: SPERMIDINE
+Macromolecule #86: HYGROMYCIN B
+Macromolecule #87: 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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| Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 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: 1.5 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Homo sapiens (human)
Authors
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Processing
FIELD EMISSION GUN
