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Open data
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Basic information
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| Title | In situ HHT and CHX treated human P-Z state 80S ribosome | |||||||||
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Keywords | In situ / Ribosome | |||||||||
| Function / homology | Function and homology informationnegative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / 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 / ribosomal protein import into nucleus ...negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / 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 / ribosomal protein import into nucleus / oxidized pyrimidine DNA binding / response to TNF agonist / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of base-excision repair / 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 / 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 / laminin receptor activity / protein kinase A binding / 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 / male meiosis I / 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 / cellular response to ethanol / regulation of cell division / 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 / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / protein serine/threonine kinase inhibitor activity / ubiquitin ligase inhibitor activity / Viral mRNA Translation / positive regulation of signal transduction by p53 class mediator / negative regulation of respiratory burst involved in inflammatory response / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / positive regulation of protein binding / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.89 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_71378.map.gz | 255.7 MB | EMDB map data format | |
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| Header (meta data) | emd-71378-v30.xml emd-71378.xml | 104.5 KB 104.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_71378_fsc.xml | 17 KB | Display | FSC data file |
| Images | emd_71378.png | 18.8 KB | ||
| Filedesc metadata | emd-71378.cif.gz | 20.1 KB | ||
| Others | emd_71378_half_map_1.map.gz emd_71378_half_map_2.map.gz | 475.4 MB 475.5 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-71378 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-71378 | HTTPS FTP |
-Validation report
| Summary document | emd_71378_validation.pdf.gz | 1.4 MB | Display | EMDB validaton report |
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| Full document | emd_71378_full_validation.pdf.gz | 1.4 MB | Display | |
| Data in XML | emd_71378_validation.xml.gz | 26.9 KB | Display | |
| Data in CIF | emd_71378_validation.cif.gz | 35.4 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-71378 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-71378 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9p8iMC ![]() 9p6zC ![]() 9p72C ![]() 9p73C ![]() 9p76C ![]() 9p7fC ![]() 9p7gC ![]() 9p7hC ![]() 9p7iC ![]() 9p7jC ![]() 9p7kC ![]() 9p7lC ![]() 9p7nC ![]() 9p7oC ![]() 9p7wC ![]() 9p7xC ![]() 9p7yC ![]() 9p8bC ![]() 9p8hC ![]() 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_71378.map.gz / Format: CCP4 / Size: 512 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: 1.068 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_71378_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_71378_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : In situ HHT and CHX treated human P-Z state 80S ribosome
+Supramolecule #1: In situ HHT and CHX treated human P-Z state 80S ribosome
+Macromolecule #1: P site tRNA [Homo sapiens]
+Macromolecule #2: 28S rRNA [Homo sapiens]
+Macromolecule #3: 5S rRNA [Homo sapiens]
+Macromolecule #4: 5.8S rRNA [Homo sapiens]
+Macromolecule #82: 18S rRNA [Homo sapiens]
+Macromolecule #83: Z site tRNA [Homo sapiens]
+Macromolecule #5: 60S ribosomal protein L8
+Macromolecule #6: Large ribosomal subunit protein uL3
+Macromolecule #7: 60S ribosomal protein L4
+Macromolecule #8: Large ribosomal subunit protein uL18
+Macromolecule #9: Large ribosomal subunit protein eL6
+Macromolecule #10: 60S ribosomal protein L7
+Macromolecule #11: 60S ribosomal protein L7a
+Macromolecule #12: 60S ribosomal protein L9
+Macromolecule #13: Ribosomal protein uL16-like
+Macromolecule #14: 60S ribosomal protein L11
+Macromolecule #15: Large ribosomal subunit protein eL13
+Macromolecule #16: 60S ribosomal protein L14
+Macromolecule #17: 60S ribosomal protein L15
+Macromolecule #18: 60S ribosomal protein L13a
+Macromolecule #19: 60S ribosomal protein L17
+Macromolecule #20: 60S ribosomal protein L18
+Macromolecule #21: 60S ribosomal protein L19
+Macromolecule #22: 60S ribosomal protein L18a
+Macromolecule #23: 60S ribosomal protein L21
+Macromolecule #24: Heparin-binding protein HBp15
+Macromolecule #25: 60S ribosomal protein L23
+Macromolecule #26: Ribosomal protein L24
+Macromolecule #27: 60S ribosomal protein L23a
+Macromolecule #28: 60S ribosomal protein L26
+Macromolecule #29: 60S ribosomal protein L27
+Macromolecule #30: 60S ribosomal protein L27a
+Macromolecule #31: Large ribosomal subunit protein eL29
+Macromolecule #32: 60S ribosomal protein L30
+Macromolecule #33: 60S ribosomal protein L31
+Macromolecule #34: 60S ribosomal protein L32
+Macromolecule #35: 60S ribosomal protein L35a
+Macromolecule #36: 60S ribosomal protein L34
+Macromolecule #37: 60S ribosomal protein L35
+Macromolecule #38: 60S ribosomal protein L36
+Macromolecule #39: 60S ribosomal protein L37
+Macromolecule #40: 60S ribosomal protein L38
+Macromolecule #41: 60S ribosomal protein L39
+Macromolecule #42: Large ribosomal subunit protein eL40
+Macromolecule #43: 60S ribosomal protein L41
+Macromolecule #44: 60S ribosomal protein L36a
+Macromolecule #45: 60S ribosomal protein L37a
+Macromolecule #46: 60S ribosomal protein L28
+Macromolecule #47: 60S acidic ribosomal protein P0
+Macromolecule #48: Large ribosomal subunit protein uL11
+Macromolecule #49: Small ribosomal subunit protein uS3
+Macromolecule #50: 40S ribosomal protein S5
+Macromolecule #51: 40S ribosomal protein S10
+Macromolecule #52: Small ribosomal subunit protein eS12
+Macromolecule #53: Small ribosomal subunit protein uS19
+Macromolecule #54: Small ribosomal subunit protein uS9
+Macromolecule #55: Small ribosomal subunit protein eS17
+Macromolecule #56: 40S ribosomal protein S18
+Macromolecule #57: 40S ribosomal protein S19
+Macromolecule #58: 40S ribosomal protein S20
+Macromolecule #59: Small ribosomal subunit protein eS25
+Macromolecule #60: 40S ribosomal protein S28
+Macromolecule #61: 40S ribosomal protein S29
+Macromolecule #62: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #63: Receptor of activated protein C kinase 1
+Macromolecule #64: 40S ribosomal protein SA
+Macromolecule #65: 40S ribosomal protein S3a
+Macromolecule #66: 40S ribosomal protein S2
+Macromolecule #67: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #68: 40S ribosomal protein S6
+Macromolecule #69: Small ribosomal subunit protein eS7
+Macromolecule #70: 40S ribosomal protein S8
+Macromolecule #71: 40S ribosomal protein S9
+Macromolecule #72: 40S ribosomal protein S11
+Macromolecule #73: 40S ribosomal protein S13
+Macromolecule #74: Small ribosomal subunit protein uS11
+Macromolecule #75: Small ribosomal subunit protein eS21
+Macromolecule #76: 40S ribosomal protein S15a
+Macromolecule #77: 40S ribosomal protein S23
+Macromolecule #78: 40S ribosomal protein S24
+Macromolecule #79: 40S ribosomal protein S26
+Macromolecule #80: Small ribosomal subunit protein eS27
+Macromolecule #81: Small ribosomal subunit protein eS30
+Macromolecule #84: Transcription factor BTF3
+Macromolecule #85: MAGNESIUM ION
+Macromolecule #86: SPERMINE
+Macromolecule #87: SPERMIDINE
+Macromolecule #88: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
+Macromolecule #89: (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methy...
+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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Y (Row.)
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Processing
FIELD EMISSION GUN


