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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | In situ human Hibernating class4 80S ribosome | |||||||||
Map data | In situ human Hibernating class4 80S ribosome | |||||||||
Sample |
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Keywords | In situ / Ribosome | |||||||||
| Function / homology | Function and homology informationSynthesis of diphthamide-EEF2 / translation at postsynapse / PML body organization / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / ribosome hibernation / translation elongation factor binding / response to folic acid / SUMO binding / positive regulation of cytoplasmic translation ...Synthesis of diphthamide-EEF2 / translation at postsynapse / PML body organization / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / ribosome hibernation / translation elongation factor binding / response to folic acid / SUMO binding / positive regulation of cytoplasmic translation / response to insecticide / 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 / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / 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 / positive regulation of ubiquitin-protein transferase activity / GAIT complex / positive regulation of DNA-templated transcription initiation / negative regulation of RNA splicing / negative regulation of DNA repair / TORC2 complex binding / G1 to G0 transition / Enterobacterial factors antagonize host defense / PD-L1(CD274) glycosylation and translocation to plasma membrane / erythrocyte homeostasis / supercoiled DNA binding / regulation of establishment of cell polarity / 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 / negative regulation of phagocytosis / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / Uptake and function of diphtheria toxin / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / lncRNA binding / laminin receptor activity / negative regulation of myoblast fusion / ion channel inhibitor activity / skeletal muscle cell differentiation / protein kinase A binding / positive regulation of mitochondrial depolarization / Ribosomal scanning and start codon recognition / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / male meiosis I / Translation initiation complex formation / Dengue Virus Genome Translation and Replication / Maturation of DENV proteins / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Protein hydroxylation / TOR signaling / BH3 domain binding / negative regulation of translational frameshifting / iron-sulfur cluster binding / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / monocyte chemotaxis / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / regulation of cell division / positive regulation of GTPase activity / translational elongation / Peptide chain elongation / cellular response to ethanol / Dengue Virus Attachment and Entry / Selenocysteine synthesis / Formation of a pool of free 40S subunits / protein targeting / negative regulation of protein binding / negative regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Eukaryotic Translation Termination / protein serine/threonine kinase inhibitor activity / protein localization to nucleus / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / negative regulation of ubiquitin-dependent protein catabolic process / ubiquitin ligase inhibitor activity Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.57 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. | |||||||||
| History |
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_71338.map.gz | 258.7 MB | EMDB map data format | |
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| Header (meta data) | emd-71338-v30.xml emd-71338.xml | 111.7 KB 111.7 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_71338_fsc.xml | 16.8 KB | Display | FSC data file |
| Images | emd_71338.png | 130.7 KB | ||
| Filedesc metadata | emd-71338.cif.gz | 21.8 KB | ||
| Others | emd_71338_half_map_1.map.gz emd_71338_half_map_2.map.gz | 474.6 MB 474.6 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-71338 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-71338 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9p7dMC ![]() 9p6zC ![]() 9p72C ![]() 9p73C ![]() 9p76C ![]() 9p78C ![]() 9p79C ![]() 9p7aC ![]() 9p7cC ![]() 9p7eC ![]() 9p7fC ![]() 9p7gC ![]() 9p7hC ![]() 9p7iC ![]() 9p7jC ![]() 9p7kC ![]() 9p7lC ![]() 9p7nC ![]() 9p7oC ![]() 9p7wC ![]() 9p7xC ![]() 9p7yC ![]() 9p8bC ![]() 9p8cC ![]() 9p8hC ![]() 9p8iC ![]() 9p9hC ![]() 9p9iC ![]() 9p9jC ![]() 9p9kC ![]() 9pa7C ![]() 9pbeC ![]() 9pkgC 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_71338.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | In situ human Hibernating class4 80S ribosome | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.068 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: Half Map A
| File | emd_71338_half_map_1.map | ||||||||||||
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| Annotation | Half Map A | ||||||||||||
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| Density Histograms |
-Half map: Half Map B
| File | emd_71338_half_map_2.map | ||||||||||||
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| Annotation | Half Map B | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : In situ human Hibernating class4 80S ribosome
+Supramolecule #1: In situ human Hibernating class4 80S ribosome
+Macromolecule #1: 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 #50: 40S ribosomal protein SA
+Macromolecule #51: 40S ribosomal protein S3a
+Macromolecule #52: 40S ribosomal protein S2
+Macromolecule #53: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #54: 40S ribosomal protein S6
+Macromolecule #55: Small ribosomal subunit protein eS7
+Macromolecule #56: 40S ribosomal protein S8
+Macromolecule #57: 40S ribosomal protein S9
+Macromolecule #58: 40S ribosomal protein S11
+Macromolecule #59: 40S ribosomal protein S13
+Macromolecule #60: Small ribosomal subunit protein uS11
+Macromolecule #61: Small ribosomal subunit protein eS21
+Macromolecule #62: 40S ribosomal protein S15a
+Macromolecule #63: 40S ribosomal protein S23
+Macromolecule #64: 40S ribosomal protein S24
+Macromolecule #65: 40S ribosomal protein S26
+Macromolecule #66: Small ribosomal subunit protein eS27
+Macromolecule #67: Small ribosomal subunit protein eS30
+Macromolecule #69: Small ribosomal subunit protein eS17
+Macromolecule #70: Small ribosomal subunit protein uS3
+Macromolecule #71: 40S ribosomal protein S5
+Macromolecule #72: 40S ribosomal protein S10
+Macromolecule #73: Small ribosomal subunit protein eS12
+Macromolecule #74: Small ribosomal subunit protein uS19
+Macromolecule #75: Small ribosomal subunit protein uS9
+Macromolecule #76: 40S ribosomal protein S18
+Macromolecule #77: 40S ribosomal protein S19
+Macromolecule #78: 40S ribosomal protein S20
+Macromolecule #79: Small ribosomal subunit protein eS25
+Macromolecule #80: 40S ribosomal protein S28
+Macromolecule #81: 40S ribosomal protein S29
+Macromolecule #82: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #83: Receptor of activated protein C kinase 1
+Macromolecule #85: Elongation factor 2
+Macromolecule #86: Proliferation-associated protein 2G4
+Macromolecule #3: 28S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #5: 5.8S rRNA
+Macromolecule #68: 18S rRNA [homo sapiens]
+Macromolecule #84: E site tRNA
+Macromolecule #87: MAGNESIUM ION
+Macromolecule #88: SPERMINE
+Macromolecule #89: SPERMIDINE
+Macromolecule #90: ZINC ION
-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


