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Yorodumi- EMDB-55091: CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND ... -
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Open data
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Basic information
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| Title | CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINE | |||||||||
Map data | Consensus map | |||||||||
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Keywords | CRYO-EM STRUCTURE / HUMAN / 80S / RIBOSOME / N1-METHYLPSEUDOURIDINE | |||||||||
| Function / homology | Function and homology informationembryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV / axial mesoderm development / negative regulation of formation of translation preinitiation complex ...embryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / oxidized pyrimidine DNA binding / response to TNF agonist / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of base-excision repair / ribosomal protein import into nucleus / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / 90S preribosome assembly / protein tyrosine kinase inhibitor activity / positive regulation of endodeoxyribonuclease activity / nucleolus organization / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / alpha-beta T cell differentiation / negative regulation of DNA repair / negative regulation of RNA splicing / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / G1 to G0 transition / supercoiled DNA binding / NF-kappaB complex / neural crest cell differentiation / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / positive regulation of ubiquitin-protein transferase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / protein kinase A binding / laminin receptor activity / homeostatic process / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / macrophage chemotaxis / lung morphogenesis / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / monocyte chemotaxis / TOR signaling / negative regulation of translational frameshifting / BH3 domain binding / positive regulation of activated T cell proliferation / Protein hydroxylation / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / regulation of cell division / cellular response to ethanol / mTORC1-mediated signalling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to actinomycin D / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Eukaryotic Translation Termination / blastocyst development / positive regulation of GTPase activity / negative regulation of ubiquitin-dependent protein catabolic process / protein serine/threonine kinase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
Authors | Rajan KS / Yonath A | |||||||||
| Funding support | Israel, 1 items
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Citation | Journal: Nature / Year: 2026Title: N-Methylpseudouridine directly modulates translation dynamics. Authors: Batsheva Rozman / Karin Broennimann / K Shanmugha Rajan / Aharon Nachshon / Chiranjeet Saha / Tamar Arazi / Vishnu Mohan / Tamar Geiger / Clayton J Wollner / Justin M Richner / Eric Westhof ...Authors: Batsheva Rozman / Karin Broennimann / K Shanmugha Rajan / Aharon Nachshon / Chiranjeet Saha / Tamar Arazi / Vishnu Mohan / Tamar Geiger / Clayton J Wollner / Justin M Richner / Eric Westhof / Ada Yonath / Anat Bashan / Noam Stern-Ginossar / ![]() Abstract: The considerable success of mRNA vaccines against SARS-CoV-2 has underscored the potential of synthetic mRNA as a transformative biomedical technology. A critical feature of this approach is the ...The considerable success of mRNA vaccines against SARS-CoV-2 has underscored the potential of synthetic mRNA as a transformative biomedical technology. A critical feature of this approach is the incorporation of the modified nucleoside N-methylpseudouridine (mΨ), which enhances antigen expression while reducing immunogenicity. However, a comprehensive understanding of how mΨ influences translation remains incomplete. Here we use ribosome profiling at the subcodon resolution to show that mΨ increases ribosome density on synthetic mRNAs, leading to higher protein production independent of innate immune activation or eIF2α phosphorylation. We find that mΨ directly slows ribosome movement in defined sequence contexts while simultaneously promoting translation initiation. Structural studies using cryo-electron microscopy reveal that mΨ alters interactions within the ribosomal decoding centre, providing a mechanistic basis for slowed elongation. Furthermore, by introducing synonymous recoding that disrupts the modification-mediated changes in elongation, we show that the mΨ-dependent enhancement of protein output is modulated by codon composition, and that mΨ impact is strongest in mRNAs containing non-optimal codons with uridines at the wobble position. Together, these findings demonstrate that mΨ directly modulates translation dynamics, thereby increasing protein yield from synthetic mRNAs in specific sequence contexts. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_55091.map.gz | 73.3 MB | EMDB map data format | |
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| Header (meta data) | emd-55091-v30.xml emd-55091.xml | 106.7 KB 106.7 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_55091_fsc.xml | 16.9 KB | Display | FSC data file |
| Images | emd_55091.png | 69.2 KB | ||
| Filedesc metadata | emd-55091.cif.gz | 21.6 KB | ||
| Others | emd_55091_half_map_1.map.gz emd_55091_half_map_2.map.gz | 337 MB 337 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-55091 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-55091 | HTTPS FTP |
-Validation report
| Summary document | emd_55091_validation.pdf.gz | 992.8 KB | Display | EMDB validaton report |
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| Full document | emd_55091_full_validation.pdf.gz | 992.3 KB | Display | |
| Data in XML | emd_55091_validation.xml.gz | 24.8 KB | Display | |
| Data in CIF | emd_55091_validation.cif.gz | 33 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-55091 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-55091 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9spiMC ![]() 9spfC 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_55091.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Consensus map | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.8245 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: Halfmap
| File | emd_55091_half_map_1.map | ||||||||||||
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| Annotation | Halfmap | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Halfmap
| File | emd_55091_half_map_2.map | ||||||||||||
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| Annotation | Halfmap | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND ...
+Supramolecule #1: CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND ...
+Macromolecule #1: tRNA-Ile-AAT-9-1
+Macromolecule #2: E site tRNA
+Macromolecule #3: 28S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #5: 5.8S rRNA
+Macromolecule #48: Synthetic mRNA
+Macromolecule #49: P site tRNA Arg-ACG
+Macromolecule #50: 18S rRNA
+Macromolecule #6: Large ribosomal subunit protein uL2
+Macromolecule #7: Large ribosomal subunit protein uL3
+Macromolecule #8: 60S ribosomal protein L4
+Macromolecule #9: 60S ribosomal protein L5
+Macromolecule #10: Large ribosomal subunit protein eL6
+Macromolecule #11: Large ribosomal subunit protein uL30
+Macromolecule #12: 60S ribosomal protein L7a
+Macromolecule #13: 60S ribosomal protein L9
+Macromolecule #14: 60S ribosomal protein L10
+Macromolecule #15: 60S ribosomal protein L11
+Macromolecule #16: Large ribosomal subunit protein eL13
+Macromolecule #17: 60S ribosomal protein L14
+Macromolecule #18: 60S ribosomal protein L15
+Macromolecule #19: 60S ribosomal protein L13a
+Macromolecule #20: 60S ribosomal protein L17
+Macromolecule #21: 60S ribosomal protein L18
+Macromolecule #22: 60S ribosomal protein L19
+Macromolecule #23: 60S ribosomal protein L18a
+Macromolecule #24: 60S ribosomal protein L21
+Macromolecule #25: 60S ribosomal protein L22
+Macromolecule #26: 60S ribosomal protein L23
+Macromolecule #27: 60S ribosomal protein L24
+Macromolecule #28: 60S ribosomal protein L23a
+Macromolecule #29: 60S ribosomal protein L26
+Macromolecule #30: 60S ribosomal protein L27
+Macromolecule #31: Large ribosomal subunit protein uL15
+Macromolecule #32: Large ribosomal subunit protein eL29
+Macromolecule #33: 60S ribosomal protein L30
+Macromolecule #34: 60S ribosomal protein L31
+Macromolecule #35: 60S ribosomal protein L32
+Macromolecule #36: 60S ribosomal protein L35a
+Macromolecule #37: 60S ribosomal protein L34
+Macromolecule #38: 60S ribosomal protein L35
+Macromolecule #39: 60S ribosomal protein L36
+Macromolecule #40: Large ribosomal subunit protein eL37
+Macromolecule #41: 60S ribosomal protein L38
+Macromolecule #42: 60S ribosomal protein L39
+Macromolecule #43: Ubiquitin-ribosomal protein eL40 fusion protein
+Macromolecule #44: 60S ribosomal protein L41
+Macromolecule #45: Large ribosomal subunit protein eL42
+Macromolecule #46: 60S ribosomal protein L37a
+Macromolecule #47: 60S ribosomal protein L28
+Macromolecule #51: 40S ribosomal protein SA
+Macromolecule #52: 40S ribosomal protein S3a
+Macromolecule #53: 40S ribosomal protein S2
+Macromolecule #54: 40S ribosomal protein S3
+Macromolecule #55: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #56: 40S ribosomal protein S5
+Macromolecule #57: 40S ribosomal protein S6
+Macromolecule #58: 40S ribosomal protein S7
+Macromolecule #59: 40S ribosomal protein S8
+Macromolecule #60: 40S ribosomal protein S9
+Macromolecule #61: 40S ribosomal protein S10
+Macromolecule #62: 40S ribosomal protein S11
+Macromolecule #63: 40S ribosomal protein S12
+Macromolecule #64: 40S ribosomal protein S13
+Macromolecule #65: 40S ribosomal protein S14
+Macromolecule #66: 40S ribosomal protein S15
+Macromolecule #67: 40S ribosomal protein S16
+Macromolecule #68: 40S ribosomal protein S17
+Macromolecule #69: 40S ribosomal protein S18
+Macromolecule #70: 40S ribosomal protein S19
+Macromolecule #71: 40S ribosomal protein S20
+Macromolecule #72: 40S ribosomal protein S21
+Macromolecule #73: 40S ribosomal protein S15a
+Macromolecule #74: 40S ribosomal protein S23
+Macromolecule #75: 40S ribosomal protein S24
+Macromolecule #76: 40S ribosomal protein S25
+Macromolecule #77: 40S ribosomal protein S26
+Macromolecule #78: 40S ribosomal protein S27
+Macromolecule #79: 40S ribosomal protein S28
+Macromolecule #80: 40S ribosomal protein S29
+Macromolecule #81: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #82: Ubiquitin
+Macromolecule #83: Receptor of activated protein C kinase 1
+Macromolecule #84: 1,4-DIAMINOBUTANE
+Macromolecule #85: SPERMIDINE
+Macromolecule #86: MAGNESIUM ION
+Macromolecule #87: POTASSIUM ION
+Macromolecule #88: ZINC ION
+Macromolecule #89: HYGROMYCIN B
+Macromolecule #90: 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: 7.6 |
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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.077 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: 1.7 µm / Nominal defocus min: 0.6 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
Israel, 1 items
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Y (Row.)
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Processing
FIELD EMISSION GUN


