[English] 日本語
Yorodumi- EMDB-71334: In situ human Hibernating rotate 3 with E-site tRNA state 80S ribosome -
+
Open data
-
Basic information
| Entry | ![]() | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Title | In situ human Hibernating rotate 3 with E-site tRNA state 80S ribosome | |||||||||
Map data | In situ human Hibernating rotate 3 with E-site tRNA state 80S ribosome | |||||||||
Sample |
| |||||||||
Keywords | In situ / Ribosome | |||||||||
| Function / homology | Function and homology informationSynthesis of diphthamide-EEF2 / translation at postsynapse / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / ribosome hibernation / translation elongation factor binding / PML body organization / response to folic acid / SUMO binding / response to insecticide ...Synthesis of diphthamide-EEF2 / translation at postsynapse / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / ribosome hibernation / translation elongation factor binding / PML body organization / response to folic acid / SUMO binding / response to insecticide / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV / positive regulation of cytoplasmic translation / 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 / aggresome / 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 / lncRNA binding / homeostatic process / ion channel inhibitor activity / Uptake and function of diphtheria toxin / 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 / skeletal muscle cell differentiation / 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) / translational elongation / 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 Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Wei Z / Yong X | |||||||||
| Funding support | 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2025Title: Visualizing the translation landscape in human cells at high resolution Authors: Zheng W / Zhang Y / Wang J / Wang S / Chai P / Bailey EJ / Zhu C / Guo W / Devarkar SC / Wu S / Lin J / Zhang K / Liu J / Lomakin IB / Xiong Y | |||||||||
| History |
|
-
Structure visualization
| Supplemental images |
|---|
-
Downloads & links
-EMDB archive
| Map data | emd_71334.map.gz | 258 MB | EMDB map data format | |
|---|---|---|---|---|
| Header (meta data) | emd-71334-v30.xml emd-71334.xml | 108.3 KB 108.3 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_71334_fsc.xml | 16.9 KB | Display | FSC data file |
| Images | emd_71334.png | 125.8 KB | ||
| Filedesc metadata | emd-71334.cif.gz | 21.3 KB | ||
| Others | emd_71334_half_map_1.map.gz emd_71334_half_map_2.map.gz | 474.4 MB 474.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-71334 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-71334 | HTTPS FTP |
-Validation report
| Summary document | emd_71334_validation.pdf.gz | 1.4 MB | Display | EMDB validaton report |
|---|---|---|---|---|
| Full document | emd_71334_full_validation.pdf.gz | 1.4 MB | Display | |
| Data in XML | emd_71334_validation.xml.gz | 26.7 KB | Display | |
| Data in CIF | emd_71334_validation.cif.gz | 35.4 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-71334 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-71334 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9p78MC ![]() 9p79C ![]() 9p7aC ![]() 9p7cC ![]() 9p7dC ![]() 9p7eC ![]() 9p8cC M: atomic model generated by this map C: citing same article ( |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
|---|---|
| Related items in Molecule of the Month |
-
Map
| File | Download / File: emd_71334.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | In situ human Hibernating rotate 3 with E-site tRNA state 80S ribosome | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.068 Å | ||||||||||||||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||||||||||||||
| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
|
-Supplemental data
-Half map: Half Map A
| File | emd_71334_half_map_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Half Map A | ||||||||||||
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-Half map: Half Map B
| File | emd_71334_half_map_2.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Half Map B | ||||||||||||
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-
Sample components
+Entire : In situ human Hibernating rotate 3 with E-site tRNA state 80S ribosome
+Supramolecule #1: In situ human Hibernating rotate 3 with E-site tRNA state 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
+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 |
|---|---|
Processing | single particle reconstruction |
| Aggregation state | cell |
-
Sample preparation
| Buffer | pH: 7.4 |
|---|---|
| Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
| Microscope | FEI TECNAI F30 |
|---|---|
| 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 |
Movie
Controller
About Yorodumi



Keywords
Homo sapiens (human)
Authors
Citation



















































Z (Sec.)
Y (Row.)
X (Col.)






































Processing
FIELD EMISSION GUN


