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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | In situ human 80S ribosome (composite map) | |||||||||
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Keywords | Ribosome / In situ | |||||||||
| Function / homology | Function and homology informationnegative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / ribosome hibernation / translation elongation factor binding / PML body organization / SUMO binding / response to insecticide / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / negative regulation of formation of translation preinitiation complex ...negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / ribosome hibernation / translation elongation factor binding / PML body organization / SUMO binding / response to insecticide / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / negative regulation of formation of translation preinitiation complex / axial mesoderm development / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus / regulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of ubiquitin-protein transferase activity / 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 gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / nucleolus organization / positive regulation of DNA-templated transcription initiation / TNFR1-mediated ceramide production / 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 / NF-kappaB complex / negative regulation of DNA repair / G1 to G0 transition / cytoplasmic translational initiation / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / rRNA modification in the nucleus and cytosol / 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 / laminin receptor activity / protein kinase A binding / homeostatic process / pigmentation / Ribosomal scanning and start codon recognition / 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 / male meiosis I / monocyte chemotaxis / BH3 domain binding / Protein hydroxylation / negative regulation of translational frameshifting / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / TOR signaling / positive regulation of GTPase activity / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / iron-sulfur cluster binding / regulation of cell division / Peptide chain elongation / cellular response to ethanol / Selenocysteine synthesis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Formation of a pool of free 40S subunits / negative regulation of protein binding / protein serine/threonine kinase inhibitor activity / Eukaryotic Translation Termination / blastocyst development / ubiquitin ligase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of respiratory burst involved in inflammatory response / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Viral mRNA Translation / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus / negative regulation of ubiquitin-dependent protein catabolic process / 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 / protein targeting / Major pathway of rRNA processing in the nucleolus and cytosol Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.19 Å | |||||||||
Authors | Wei Z / Yong X | |||||||||
| Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2025Title: Visualizing the translation landscape in human cells at high resolution. Authors: Wei Zheng / Yuekang Zhang / Jimin Wang / Shuhui Wang / Pengxin Chai / Elizabeth J Bailey / Chenghao Zhu / Wangbiao Guo / Swapnil C Devarkar / Shenping Wu / Jianfeng Lin / Kai Zhang / Jun Liu ...Authors: Wei Zheng / Yuekang Zhang / Jimin Wang / Shuhui Wang / Pengxin Chai / Elizabeth J Bailey / Chenghao Zhu / Wangbiao Guo / Swapnil C Devarkar / Shenping Wu / Jianfeng Lin / Kai Zhang / Jun Liu / Ivan B Lomakin / Yong Xiong / ![]() Abstract: Comprehensive in situ structures of macromolecules can transform our understanding of biology and advance human health. Here, we map protein synthesis inside human cells in detail by combining ...Comprehensive in situ structures of macromolecules can transform our understanding of biology and advance human health. Here, we map protein synthesis inside human cells in detail by combining automated cryo-focused ion beam (FIB) milling and in situ single-particle cryo electron microscopy (cryo-EM). With this in situ cryo-EM approach, we resolved a 2.2 Å consensus structure of the human 80S ribosome and unveiled 23 functional states, nearly all better than 3 Å resolution. Compared to in vitro studies, we observed variations in ribosome structures, distinct environments of ion and polyamine binding, and associated proteins such as EDF1 and NACβ that are typically not enriched with purified ribosomes. We also detected additional peptide-related density features on the ribosome and visualized ribosome-ribosome interactions in helical polysomes. Finally, high-resolution structures from cells treated with homoharringtonine and cycloheximide revealed a distinct translational landscape and a spermidine that interacts with cycloheximide at the E site, one of the numerous polyamines that also bind native ribosomes. These results underscore the value of high-resolution in situ studies in the native environment. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_71477.map.gz | 46.7 MB | EMDB map data format | |
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| Header (meta data) | emd-71477-v30.xml emd-71477.xml | 108.3 KB 108.3 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_71477_fsc.xml | 18.9 KB | Display | FSC data file |
| Images | emd_71477.png | 171.1 KB | ||
| Filedesc metadata | emd-71477.cif.gz | 20.6 KB | ||
| Others | emd_71477_half_map_1.map.gz emd_71477_half_map_2.map.gz | 676.1 MB 676.1 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-71477 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-71477 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9pbeMC ![]() 9p6zC ![]() 9p72C ![]() 9p73C ![]() 9p76C ![]() 9p78C ![]() 9p79C ![]() 9p7aC ![]() 9p7cC ![]() 9p7dC ![]() 9p7eC ![]() 9p7fC ![]() 9p7gC ![]() 9p7hC ![]() 9p7iC ![]() 9p7jC ![]() 9p7kC ![]() 9p7lC ![]() 9p7nC ![]() 9p7oC ![]() 9p7wC ![]() 9p7xC ![]() 9p7yC ![]() 9p8bC ![]() 9p8cC ![]() 9p8hC ![]() 9p8iC ![]() 9p9hC ![]() 9p9iC ![]() 9p9jC ![]() 9p9kC ![]() 9pa7C ![]() 9pkgC C: citing same article ( M: atomic model generated by this map |
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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_71477.map.gz / Format: CCP4 / Size: 729 MB / 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: 0.89 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_71477_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_71477_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : In situ human 80S ribosome (composite map)
+Supramolecule #1: In situ human 80S ribosome (composite map)
+Macromolecule #1: Isoform 2 of SERPINE1 mRNA-binding protein 1
+Macromolecule #2: Transcription factor BTF3
+Macromolecule #6: 60S ribosomal protein L8
+Macromolecule #7: Large ribosomal subunit protein uL3
+Macromolecule #8: 60S ribosomal protein L4
+Macromolecule #9: Large ribosomal subunit protein uL18
+Macromolecule #10: Large ribosomal subunit protein eL6
+Macromolecule #11: 60S ribosomal protein L7
+Macromolecule #12: 60S ribosomal protein L7a
+Macromolecule #13: 60S ribosomal protein L9
+Macromolecule #14: Ribosomal protein uL16-like
+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: Heparin-binding protein HBp15
+Macromolecule #26: 60S ribosomal protein L23
+Macromolecule #27: Ribosomal protein L24
+Macromolecule #28: 60S ribosomal protein L23a
+Macromolecule #29: 60S ribosomal protein L26
+Macromolecule #30: 60S ribosomal protein L27
+Macromolecule #31: 60S ribosomal protein L27a
+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: 60S ribosomal protein L37
+Macromolecule #41: 60S ribosomal protein L38
+Macromolecule #42: 60S ribosomal protein L39
+Macromolecule #43: Large ribosomal subunit protein eL40
+Macromolecule #44: 60S ribosomal protein L41
+Macromolecule #45: 60S ribosomal protein L36a
+Macromolecule #46: 60S ribosomal protein L37a
+Macromolecule #47: 60S ribosomal protein L28
+Macromolecule #48: 60S acidic ribosomal protein P0
+Macromolecule #49: Large ribosomal subunit protein uL11
+Macromolecule #52: 40S ribosomal protein SA
+Macromolecule #53: 40S ribosomal protein S3a
+Macromolecule #54: 40S ribosomal protein S2
+Macromolecule #55: Small ribosomal subunit protein uS3
+Macromolecule #56: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #57: 40S ribosomal protein S5
+Macromolecule #58: 40S ribosomal protein S6
+Macromolecule #59: Small ribosomal subunit protein eS7
+Macromolecule #60: 40S ribosomal protein S8
+Macromolecule #61: 40S ribosomal protein S9
+Macromolecule #62: 40S ribosomal protein S10
+Macromolecule #63: 40S ribosomal protein S11
+Macromolecule #64: Small ribosomal subunit protein eS12
+Macromolecule #65: 40S ribosomal protein S13
+Macromolecule #66: Small ribosomal subunit protein uS11
+Macromolecule #67: Small ribosomal subunit protein uS19
+Macromolecule #68: Small ribosomal subunit protein uS9
+Macromolecule #69: Small ribosomal subunit protein eS17
+Macromolecule #70: 40S ribosomal protein S18
+Macromolecule #71: 40S ribosomal protein S19
+Macromolecule #72: 40S ribosomal protein S20
+Macromolecule #73: Small ribosomal subunit protein eS21
+Macromolecule #74: 40S ribosomal protein S15a
+Macromolecule #75: 40S ribosomal protein S23
+Macromolecule #76: 40S ribosomal protein S24
+Macromolecule #77: Small ribosomal subunit protein eS25
+Macromolecule #78: 40S ribosomal protein S26
+Macromolecule #79: Small ribosomal subunit protein eS27
+Macromolecule #80: 40S ribosomal protein S28
+Macromolecule #81: 40S ribosomal protein S29
+Macromolecule #82: Small ribosomal subunit protein eS30
+Macromolecule #83: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #84: Receptor of activated protein C kinase 1
+Macromolecule #3: 28S rRNA
+Macromolecule #4: 5S rRNA [Homo sapiens]
+Macromolecule #5: 5.8S rRNA [Homo sapiens]
+Macromolecule #50: P site tRNA
+Macromolecule #51: 18S rRNA
+Macromolecule #85: MAGNESIUM ION
+Macromolecule #86: SPERMINE
+Macromolecule #87: SPERMIDINE
+Macromolecule #88: POTASSIUM ION
+Macromolecule #89: ZINC ION
+Macromolecule #90: 1,4-DIAMINOBUTANE
+Macromolecule #91: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | cell |
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Sample preparation
| Buffer | pH: 7.4 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI TECNAI F30 |
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| Image recording | Film or detector model: GATAN K3 (6k 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: 2.5 µm / Nominal defocus min: 1.2 µm |
| Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Homo sapiens (human)
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Processing
FIELD EMISSION GUN


