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Yorodumi- EMDB-50673: CRYO-EM STRUCTURE OF HCT15 POLYSOMES BOUND TO EEF2, EBP1, AND SERBP1 -
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Open data
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Basic information
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| Title | CRYO-EM STRUCTURE OF HCT15 POLYSOMES BOUND TO EEF2, EBP1, AND SERBP1 | |||||||||
Map data | COMPOSITE MAP | |||||||||
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Keywords | CRYO-EM / HCT15 cancer cell / POLYSOMES / dormant ribosome / hybernating ribosome / RIBOSOME | |||||||||
| Function / homology | Function and homology informationSynthesis of diphthamide-EEF2 / translation at postsynapse / ribosome hibernation / translation elongation factor binding / PML body organization / response to folic acid / SUMO binding / translation at presynapse / exit from mitosis / optic nerve development ...Synthesis of diphthamide-EEF2 / translation at postsynapse / ribosome hibernation / translation elongation factor binding / PML body organization / response to folic acid / SUMO binding / translation at presynapse / exit from mitosis / optic nerve development / 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 / retinal ganglion cell axon guidance / oxidized pyrimidine DNA binding / response to TNF agonist / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of base-excision repair / ribosomal protein import into nucleus / 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 / alpha-beta T cell differentiation / 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 / protein kinase A binding / laminin receptor activity / homeostatic process / ion channel inhibitor activity / lncRNA binding / 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 / Protein hydroxylation / positive regulation of activated T cell proliferation / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / regulation of cell division / cellular response to ethanol / 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 Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | |||||||||
Authors | Rajan KS / Yonath A | |||||||||
| Funding support | 1 items
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Citation | Journal: To Be PublishedTitle: CRYO-EM STRUCTURE OF HCT15 POLYSOMES BOUND TO EEF2, EBP1, AND SERBP1 Authors: Rajan KS / Yonath A | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_50673.map.gz | 43 MB | EMDB map data format | |
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| Header (meta data) | emd-50673-v30.xml emd-50673.xml | 106.3 KB 106.3 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_50673_fsc.xml | 17 KB | Display | FSC data file |
| Images | emd_50673.png | 105.6 KB | ||
| Filedesc metadata | emd-50673.cif.gz | 22.4 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50673 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50673 | HTTPS FTP |
-Validation report
| Summary document | emd_50673_validation.pdf.gz | 525.8 KB | Display | EMDB validaton report |
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| Full document | emd_50673_full_validation.pdf.gz | 525.3 KB | Display | |
| Data in XML | emd_50673_validation.xml.gz | 15.5 KB | Display | |
| Data in CIF | emd_50673_validation.cif.gz | 21.4 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50673 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50673 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9fqzMC 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_50673.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | COMPOSITE MAP | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.8245 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : CRYO-EM STRUCTURE OF HCT15 POLYSOMES BOUND TO EEF2, EBP1, AND SERBP1
+Supramolecule #1: CRYO-EM STRUCTURE OF HCT15 POLYSOMES BOUND TO EEF2, EBP1, AND SERBP1
+Macromolecule #1: Elongation factor 2
+Macromolecule #3: Isoform 2 of SERPINE1 mRNA-binding protein 1
+Macromolecule #5: 60S ribosomal protein L8
+Macromolecule #6: 60S ribosomal protein L3
+Macromolecule #7: 60S ribosomal protein L4
+Macromolecule #8: 60S ribosomal protein L5
+Macromolecule #9: 60S ribosomal protein L6
+Macromolecule #10: Large ribosomal subunit protein uL30
+Macromolecule #11: 60S ribosomal protein L7a
+Macromolecule #12: 60S ribosomal protein L9
+Macromolecule #13: 60S ribosomal protein L10-like
+Macromolecule #14: 60S ribosomal protein L11
+Macromolecule #15: 60S ribosomal protein L13
+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: 60S ribosomal protein L22
+Macromolecule #25: 60S ribosomal protein L23
+Macromolecule #26: 60S 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: 60S ribosomal protein L29
+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: Ubiquitin-60S ribosomal protein L40
+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 #48: 40S ribosomal protein SA
+Macromolecule #49: 40S ribosomal protein S3a
+Macromolecule #50: 40S ribosomal protein S2
+Macromolecule #51: 40S ribosomal protein S3
+Macromolecule #52: 40S ribosomal protein S4, X isoform
+Macromolecule #53: 40S ribosomal protein S5
+Macromolecule #54: 40S ribosomal protein S6
+Macromolecule #55: 40S ribosomal protein S7
+Macromolecule #56: 40S ribosomal protein S8
+Macromolecule #57: 40S ribosomal protein S9
+Macromolecule #58: 40S ribosomal protein S10
+Macromolecule #59: 40S ribosomal protein S11
+Macromolecule #60: 40S ribosomal protein S12
+Macromolecule #61: 40S ribosomal protein S13
+Macromolecule #62: 40S ribosomal protein S14
+Macromolecule #63: 40S ribosomal protein S15
+Macromolecule #64: 40S ribosomal protein S16
+Macromolecule #65: 40S ribosomal protein S17
+Macromolecule #66: 40S ribosomal protein S18
+Macromolecule #67: 40S ribosomal protein S19
+Macromolecule #68: 40S ribosomal protein S20
+Macromolecule #69: 40S ribosomal protein S21
+Macromolecule #70: 40S ribosomal protein S15a
+Macromolecule #71: 40S ribosomal protein S23
+Macromolecule #72: 40S ribosomal protein S24
+Macromolecule #73: 40S ribosomal protein S25
+Macromolecule #74: 40S ribosomal protein S26
+Macromolecule #75: 40S ribosomal protein S27
+Macromolecule #76: 40S ribosomal protein S28
+Macromolecule #77: 40S ribosomal protein S29
+Macromolecule #78: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #79: Ubiquitin
+Macromolecule #80: Receptor of activated protein C kinase 1
+Macromolecule #83: 60S acidic ribosomal protein P0
+Macromolecule #84: Proliferation-associated protein 2G4
+Macromolecule #2: tRNA
+Macromolecule #4: 5.8S rRNA
+Macromolecule #47: SSU rRNA
+Macromolecule #81: LSU rRNA
+Macromolecule #82: 5S rRNA
+Macromolecule #85: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #86: MAGNESIUM ION
+Macromolecule #87: POTASSIUM ION
+Macromolecule #88: ZINC ION
+Macromolecule #89: 1,4-DIAMINOBUTANE
+Macromolecule #90: HYGROMYCIN B
+Macromolecule #91: SPERMIDINE
+Macromolecule #92: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
+Macromolecule #93: ANISOMYCIN
+Macromolecule #94: SODIUM ION
+Macromolecule #95: water
-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: 7.6 |
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| Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 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: 1.7 µm / Nominal defocus min: 0.6 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Keywords
Homo sapiens (human)
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Processing
FIELD EMISSION GUN


