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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | Rabbit 60S ribosomal subunit with eEF2 domain IV open | |||||||||
Map data | 60S_eEF2_OPEN_main_map_no_mask_applied. This contour level selected to avoid too much noises which resulted in low density visible for chains u, t, ES. please see the softened map description. | |||||||||
Sample |
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Keywords | Ribosome / Hibernation / In extracto Cryo EM / Rabbit | |||||||||
| Function / homology | Function and homology informationubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of cell differentiation / cytoplasmic ribonucleoprotein granule / rRNA processing / azurophil granule lumen ...ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of cell differentiation / cytoplasmic ribonucleoprotein granule / rRNA processing / azurophil granule lumen / transcription corepressor activity / regulation of translation / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit rRNA binding / killing of cells of another organism / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / nucleic acid binding / cytoplasmic translation / tRNA binding / postsynaptic density / negative regulation of translation / rRNA binding / ribosome / translation / structural constituent of ribosome / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / mRNA binding / negative regulation of apoptotic process / Neutrophil degranulation / nucleolus / synapse / endoplasmic reticulum / DNA-templated transcription / RNA binding / extracellular exosome / extracellular region / zinc ion binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Seraj Z / Zottig X / Huang CH / Loveland AB / Diggs S / Sholi E / Grigorieff N / Korostelev AA | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: To Be PublishedTitle: In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles Authors: Seraj Z / Zottig X / Huang CH / Loveland AB / Diggs S / Sholi E / Grigorieff N / Korostelev AA | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_75704.map.gz | 1.8 GB | EMDB map data format | |
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| Header (meta data) | emd-75704-v30.xml emd-75704.xml | 76.1 KB 76.1 KB | Display Display | EMDB header |
| Images | emd_75704.png | 94.4 KB | ||
| Filedesc metadata | emd-75704.cif.gz | 16.2 KB | ||
| Others | emd_75704_additional_1.map.gz emd_75704_half_map_1.map.gz emd_75704_half_map_2.map.gz | 1.8 GB 1.8 GB 1.8 GB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-75704 ftp://data.pdbj.org/pub/emdb/structures/EMD-75704 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 11hvMC ![]() 11heC ![]() 11hgC ![]() 11iqC ![]() 11jjC ![]() 11khC 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_75704.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | 60S_eEF2_OPEN_main_map_no_mask_applied. This contour level selected to avoid too much noises which resulted in low density visible for chains u, t, ES. please see the softened map description. | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: This b-factor softened map used for modeling eEF2...
| File | emd_75704_additional_1.map | ||||||||||||
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| Annotation | This b-factor softened map used for modeling eEF2 and some poor density regions, including chain u, t, ES. | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: 60S eEF2 OPEN map1 no mask applied
| File | emd_75704_half_map_1.map | ||||||||||||
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| Annotation | 60S_eEF2_OPEN_map1_no_mask_applied | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: 60S eEF2 OPEN map2 no mask applied
| File | emd_75704_half_map_2.map | ||||||||||||
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| Annotation | 60S_eEF2_OPEN_map2_no_mask_applied | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : Rabbit Reticulocyte Lysate
+Supramolecule #1: Rabbit Reticulocyte Lysate
+Macromolecule #1: Elongation factor 2
+Macromolecule #4: 60S ribosomal protein L8
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4
+Macromolecule #7: 60S ribosomal protein L5
+Macromolecule #8: Large ribosomal subunit protein eL6
+Macromolecule #9: 60S ribosomal protein L7
+Macromolecule #10: Large ribosomal subunit protein eL8
+Macromolecule #11: 60S ribosomal protein L9
+Macromolecule #12: Ribosomal protein L10
+Macromolecule #13: 60S ribosomal protein L11
+Macromolecule #14: Large ribosomal subunit protein eL13
+Macromolecule #15: 60S ribosomal protein L14
+Macromolecule #16: 60S ribosomal protein L15
+Macromolecule #17: Large ribosomal subunit protein uL13
+Macromolecule #18: 60S ribosomal protein L17
+Macromolecule #19: 60S ribosomal protein L19
+Macromolecule #20: Large ribosomal subunit protein eL20
+Macromolecule #21: 60S ribosomal protein L21
+Macromolecule #22: Large ribosomal subunit protein eL22
+Macromolecule #23: Ribosomal protein L24
+Macromolecule #24: Large ribosomal subunit protein uL23
+Macromolecule #25: 60S ribosomal protein L26
+Macromolecule #26: 60S ribosomal protein L27
+Macromolecule #27: 60S ribosomal protein L27a
+Macromolecule #28: Large ribosomal subunit protein eL29
+Macromolecule #29: 60S ribosomal protein L30
+Macromolecule #30: 60S ribosomal protein L31
+Macromolecule #31: Large ribosomal subunit protein eL32
+Macromolecule #32: Large ribosomal subunit protein eL33
+Macromolecule #33: 60S ribosomal protein L34
+Macromolecule #34: 60S ribosomal protein L35
+Macromolecule #35: 60S ribosomal protein L36
+Macromolecule #36: 60S ribosomal protein L37
+Macromolecule #37: Large ribosomal subunit protein eL38
+Macromolecule #38: 60S ribosomal protein L39
+Macromolecule #39: Large ribosomal subunit protein eL40
+Macromolecule #40: eL42
+Macromolecule #41: 60S ribosomal protein L37a
+Macromolecule #42: 60S ribosomal protein L28
+Macromolecule #43: 60S acidic ribosomal protein P0
+Macromolecule #44: uL11
+Macromolecule #45: Proliferation-associated protein 2G4
+Macromolecule #46: 60S ribosomal protein L10a
+Macromolecule #47: Large ribosomal subunit protein eL18
+Macromolecule #50: Large ribosomal subunit protein uL14
+Macromolecule #2: 5.8S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #48: ES27L
+Macromolecule #49: 28S rRNA
+Macromolecule #51: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #52: 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: 7.3 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: OTHER / Average electron dose: 39.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
| Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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United States, 1 items
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