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Yorodumi- EMDB-65434: Cryo-EM map of the human cytosolic ribosome in a rotated state, w... -
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Basic information
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| Title | Cryo-EM map of the human cytosolic ribosome in a rotated state, with multiple neomycin molecules bound, featuring A/P-site and P/E-site tRNAs | |||||||||
Map data | Cryo-EM electron density map of the human cytosolic ribosome in a rotated state, with multiple neomycin molecules bound, featuring A/P-site and P/E-site tRNAs | |||||||||
Sample |
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Keywords | cytosolic ribosome / neomycin / RIBOSOME | |||||||||
| Function / homology | Function and homology informationtranslation at presynapse / optic nerve development / response to insecticide / alpha-beta T cell differentiation / exit from mitosis / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / negative regulation of endoplasmic reticulum unfolded protein response / regulation of G1 to G0 transition ...translation at presynapse / optic nerve development / response to insecticide / alpha-beta T cell differentiation / exit from mitosis / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / negative regulation of endoplasmic reticulum unfolded protein response / regulation of G1 to G0 transition / axial mesoderm development / retinal ganglion cell axon guidance / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / middle ear morphogenesis / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / 90S preribosome assembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / positive regulation of ubiquitin-protein transferase activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / positive regulation of DNA-templated transcription initiation / nucleolus organization / TNFR1-mediated ceramide production / negative regulation of formation of translation preinitiation complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / PD-L1(CD274) glycosylation and translocation to plasma membrane / GAIT complex / negative regulation of RNA splicing / Enterobacterial factors antagonize host defense / TORC2 complex binding / G1 to G0 transition / supercoiled DNA binding / negative regulation of DNA repair / erythrocyte homeostasis / blastocyst development / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / NF-kappaB complex / cytoplasmic translational initiation / rRNA modification in the nucleus and cytosol / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of phagocytosis / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / negative regulation of myoblast fusion / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ion channel inhibitor activity / positive regulation of natural killer cell proliferation / Maturation of DENV proteins / protein kinase A binding / homeostatic process / laminin receptor activity / lung morphogenesis / Dengue Virus Genome Translation and Replication / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Ribosomal scanning and start codon recognition / positive regulation of mitochondrial depolarization / Translation initiation complex formation / macrophage chemotaxis / negative regulation of Wnt signaling pathway / male meiosis I / fibroblast growth factor binding / Dengue Virus Attachment and Entry / Protein hydroxylation / BH3 domain binding / negative regulation of translational frameshifting / TOR signaling / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / monocyte chemotaxis / mTORC1-mediated signalling / positive regulation of GTPase activity / SARS-CoV-1 modulates host translation machinery / regulation of cell division / iron-sulfur cluster binding / cellular response to ethanol / Peptide chain elongation / 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 / protein localization to nucleus / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / protein targeting / negative regulation of respiratory burst involved in inflammatory response / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / negative regulation of ubiquitin-dependent protein catabolic process / Viral mRNA Translation Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.51 Å | |||||||||
Authors | Zhu L / Jia C / Wu M / Li W | |||||||||
| Funding support | China, 2 items
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Citation | Journal: To Be PublishedTitle: Human ribosome interactions reframe neomycin toxicity Authors: Zhang X / Zhu L / Jia C / Wu K / Bai Y / Sun S / Zhang Z / Guo L / Hou X / Wu M / Amunts A / Li W | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Header (meta data) | emd-65434-v30.xml emd-65434.xml | 105.7 KB 105.7 KB | Display Display | EMDB header |
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| FSC (resolution estimation) | emd_65434_fsc.xml | 22.4 KB | Display | FSC data file |
| Images | emd_65434.png | 122.2 KB | ||
| Map data | emd_65434.map.gz | 1.1 GB | EMDB map data format | |
| Filedesc metadata | emd-65434.cif.gz | 21 KB | ||
| Others | emd_65434_half_map_1.map.gz emd_65434_half_map_2.map.gz | 1.1 GB 1.1 GB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-65434 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-65434 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9vxnMC ![]() 65411 ![]() 65412 ![]() 65413 ![]() 65414 ![]() 65415 ![]() 65416 ![]() 65417 ![]() 65418 ![]() 65419 ![]() 65420 ![]() 65421 ![]() 65422 ![]() 65423 ![]() 65424 ![]() 65425 ![]() 65426 ![]() 65427 ![]() 65428 ![]() 65429 ![]() 65431 ![]() 65433 ![]() 9vxmC 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
-Supplemental data
-Half map: #2
| File | emd_65434_half_map_1.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
-Half map: #1
| File | emd_65434_half_map_2.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : Human cytosolic ribosome in a rotated state, with multiple neomyc...
+Supramolecule #1: Human cytosolic ribosome in a rotated state, with multiple neomyc...
+Macromolecule #1: 28S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 5.8S rRNA
+Macromolecule #46: 18S rRNA
+Macromolecule #80: A/P-tRNA
+Macromolecule #81: P/E-tRNA
+Macromolecule #82: mRNA
+Macromolecule #4: Large ribosomal subunit protein uL2
+Macromolecule #5: Large ribosomal subunit protein uL3
+Macromolecule #6: Large ribosomal subunit protein uL4
+Macromolecule #7: Large ribosomal subunit protein uL18
+Macromolecule #8: Large ribosomal subunit protein eL6
+Macromolecule #9: Large ribosomal subunit protein uL30
+Macromolecule #10: Large ribosomal subunit protein eL8
+Macromolecule #11: Large ribosomal subunit protein uL6
+Macromolecule #12: Ribosomal protein uL16-like
+Macromolecule #13: Large ribosomal subunit protein uL5
+Macromolecule #14: Large ribosomal subunit protein eL13
+Macromolecule #15: Large ribosomal subunit protein eL14
+Macromolecule #16: Large ribosomal subunit protein eL15
+Macromolecule #17: Large ribosomal subunit protein uL13
+Macromolecule #18: Large ribosomal subunit protein uL22
+Macromolecule #19: Large ribosomal subunit protein eL18
+Macromolecule #20: Large ribosomal subunit protein eL19
+Macromolecule #21: Large ribosomal subunit protein eL20
+Macromolecule #22: Large ribosomal subunit protein eL21
+Macromolecule #23: Large ribosomal subunit protein eL22
+Macromolecule #24: Large ribosomal subunit protein uL14
+Macromolecule #25: Large ribosomal subunit protein eL24
+Macromolecule #26: Large ribosomal subunit protein uL23
+Macromolecule #27: Large ribosomal subunit protein uL24
+Macromolecule #28: Large ribosomal subunit protein eL27
+Macromolecule #29: Large ribosomal subunit protein uL15
+Macromolecule #30: Large ribosomal subunit protein eL29
+Macromolecule #31: Large ribosomal subunit protein eL30
+Macromolecule #32: Large ribosomal subunit protein eL31
+Macromolecule #33: Large ribosomal subunit protein eL32
+Macromolecule #34: Large ribosomal subunit protein eL33
+Macromolecule #35: Large ribosomal subunit protein eL34
+Macromolecule #36: Large ribosomal subunit protein uL29
+Macromolecule #37: Large ribosomal subunit protein eL36
+Macromolecule #38: Large ribosomal subunit protein eL37
+Macromolecule #39: Large ribosomal subunit protein eL38
+Macromolecule #40: Large ribosomal subunit protein eL39
+Macromolecule #41: Ubiquitin-ribosomal protein eL40 fusion protein
+Macromolecule #42: Small ribosomal subunit protein eS32
+Macromolecule #43: Large ribosomal subunit protein eL42
+Macromolecule #44: Large ribosomal subunit protein eL43
+Macromolecule #45: Large ribosomal subunit protein eL28
+Macromolecule #47: Small ribosomal subunit protein uS2
+Macromolecule #48: Small ribosomal subunit protein eS1
+Macromolecule #49: Small ribosomal subunit protein uS5
+Macromolecule #50: Small ribosomal subunit protein uS3
+Macromolecule #51: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #52: Small ribosomal subunit protein uS7
+Macromolecule #53: Small ribosomal subunit protein eS6
+Macromolecule #54: Small ribosomal subunit protein eS7
+Macromolecule #55: Small ribosomal subunit protein eS8
+Macromolecule #56: Small ribosomal subunit protein uS4
+Macromolecule #57: Small ribosomal subunit protein eS10
+Macromolecule #58: Small ribosomal subunit protein uS17
+Macromolecule #59: Small ribosomal subunit protein eS12
+Macromolecule #60: Small ribosomal subunit protein uS15
+Macromolecule #61: Small ribosomal subunit protein uS11
+Macromolecule #62: Small ribosomal subunit protein uS19
+Macromolecule #63: Small ribosomal subunit protein uS9
+Macromolecule #64: Small ribosomal subunit protein eS17
+Macromolecule #65: Small ribosomal subunit protein uS13
+Macromolecule #66: Small ribosomal subunit protein eS19
+Macromolecule #67: Small ribosomal subunit protein uS10
+Macromolecule #68: Small ribosomal subunit protein eS21
+Macromolecule #69: Small ribosomal subunit protein uS8
+Macromolecule #70: Small ribosomal subunit protein uS12
+Macromolecule #71: Small ribosomal subunit protein eS24
+Macromolecule #72: Small ribosomal subunit protein eS25
+Macromolecule #73: Small ribosomal subunit protein eS26
+Macromolecule #74: Small ribosomal subunit protein eS27
+Macromolecule #75: Small ribosomal subunit protein eS28
+Macromolecule #76: Small ribosomal subunit protein uS14
+Macromolecule #77: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #78: Ubiquitin
+Macromolecule #79: Small ribosomal subunit protein RACK1
+Macromolecule #83: MAGNESIUM ION
+Macromolecule #84: POTASSIUM ION
+Macromolecule #85: SPERMIDINE
+Macromolecule #86: NEOMYCIN
+Macromolecule #87: ZINC ION
+Macromolecule #88: BETA-L-ASPARTIC ACID
-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: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 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: 2.0 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
China, 2 items
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Y (Row.)
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Processing
FIELD EMISSION GUN


