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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | Rabbit 80S with eEF2,CCDC124,and LARP1,40S-head-swiveled | |||||||||
Map data | clean Sub-class with CCDC124, eEF2 and LARP1. used for final refinement. | |||||||||
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Keywords | Ribosome / Hibernation / In extracto Cryo EM / Rabbit | |||||||||
| Function / homology | Function and homology informationSynthesis of diphthamide-EEF2 / translation at postsynapse / glial cell proliferation / skeletal muscle cell differentiation / response to folic acid / positive regulation of cytoplasmic translation / Uptake and function of diphtheria toxin / regulation of translation involved in cellular response to UV / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein-DNA complex disassembly ...Synthesis of diphthamide-EEF2 / translation at postsynapse / glial cell proliferation / skeletal muscle cell differentiation / response to folic acid / positive regulation of cytoplasmic translation / Uptake and function of diphtheria toxin / regulation of translation involved in cellular response to UV / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein-DNA complex disassembly / lncRNA binding / positive regulation of DNA damage response, signal transduction by p53 class mediator / translational elongation / Peptide chain elongation / translation elongation factor activity / response to ischemia / ubiquitin ligase inhibitor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / phagocytic cup / skeletal muscle contraction / negative regulation of ubiquitin-dependent protein catabolic process / Protein methylation / cellular response to brain-derived neurotrophic factor stimulus / translation regulator activity / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / positive regulation of apoptotic signaling pathway / MDM2/MDM4 family protein binding / response to endoplasmic reticulum stress / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / response to hydrogen peroxide / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA damage response, signal transduction by p53 class mediator / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of cell differentiation / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / cellular response to gamma radiation / spindle / cytoplasmic ribonucleoprotein granule / mRNA 5'-UTR binding / transcription coactivator binding / p53 binding / rRNA processing / actin filament binding / cytosolic ribosome / azurophil granule lumen / transcription corepressor activity / response to estradiol / glucose homeostasis / large ribosomal subunit / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / secretory granule lumen / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ficolin-1-rich granule lumen / cytosolic large ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / response to ethanol / perikaryon / nucleic acid binding / cytoplasmic translation / postsynapse / postsynaptic density / protein stabilization / rRNA binding / negative regulation of translation / mitochondrial inner membrane / response to xenobiotic stimulus / ribonucleoprotein complex / structural constituent of ribosome / cadherin binding / ribosome / translation / negative regulation of DNA-templated transcription / mRNA binding / ubiquitin protein ligase binding / centrosome / GTPase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / nucleolus / Neutrophil degranulation / dendrite / GTP binding / protein kinase binding / synapse / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / perinuclear region of 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: Elife / Year: 2026Title: cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles. Authors: Zahra Seraj / Ximena Zottig / ChunYing Huang / Anna B Loveland / Stephen Diggs / Emily Sholi / Nikolaus Grigorieff / Andrei A Korostelev / ![]() Abstract: Cryogenic electron microscopy (cryo-EM) made impressive progress in resolving cellular macromolecules and their detailed interactions. Single-particle cryo-EM traditionally relies on purified ...Cryogenic electron microscopy (cryo-EM) made impressive progress in resolving cellular macromolecules and their detailed interactions. Single-particle cryo-EM traditionally relies on purified macromolecules and lacks the complexity of cellular environments, whereas cryo-EM and cryogenic electron tomography (cryo-ET) require extensive sample preparation and data acquisition, presenting challenges in achieving high resolution. We describe cryo-EM of cellular lysates- cryo-EM-allowing the flexibility and high-resolution of cryo-EM in the context of cellular components. High-resolution 2D template matching (2DTM) yields ~2.2 Å maps of the mammalian translational apparatus. Elongating ribosome abundances in primate cell lines (MCF-7 and BSC-1) and rabbit reticulocyte lysates range from ~70% to ~10%, reflecting translational stress responses. Non-translating (hibernating) ribosomes carrying no mRNA feature numerous proteins shielding ribosomal functional centers. Elongation factor 2 (eEF2) is the most abundant hibernation factor bound to >95% of 80S ribosomes and, unexpectedly, to 60S subunits. eEF2•GDP is stabilized by interactions with the sarcin-ricin loop and protein uL14. Hibernating ribosomes also feature La-related protein 1 (LARP1) involved in initiation and mTOR signaling, eIF5A implicated in elongation and termination, and other factors, exposing the variety of hibernation scenarios. Our work underscores the efficiency and potential of cryo-EM to discover native cellular complexes and mechanisms at near-atomic resolution. | |||||||||
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_75689.map.gz | 1.8 GB | EMDB map data format | |
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| Header (meta data) | emd-75689-v30.xml emd-75689.xml | 116.7 KB 116.7 KB | Display Display | EMDB header |
| Images | emd_75689.png | 84.1 KB | ||
| Filedesc metadata | emd-75689.cif.gz | 23 KB | ||
| Others | emd_75689_additional_1.map.gz emd_75689_half_map_1.map.gz emd_75689_half_map_2.map.gz | 1.8 GB 544.9 MB 544.4 MB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-75689 ftp://data.pdbj.org/pub/emdb/structures/EMD-75689 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 11hgMC ![]() 11heC ![]() 11hvC ![]() 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_75689.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | clean Sub-class with CCDC124, eEF2 and LARP1. used for final refinement. | ||||||||||||||||||||||||||||||||||||
| 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: map for all classes with CCDC124, eEF2 and...
| File | emd_75689_additional_1.map | ||||||||||||
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| Annotation | map for all classes with CCDC124, eEF2 and LARP1. Used for rigid body fitting, specially for 40S and CCDC124. | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: #2
| File | emd_75689_half_map_1.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
-Half map: #1
| File | emd_75689_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Rabbit Reticulocyte Lysate
+Supramolecule #1: Rabbit Reticulocyte Lysate
+Macromolecule #1: 40S_SA_C domain-containing protein
+Macromolecule #2: 40S ribosomal protein S2
+Macromolecule #3: eS21
+Macromolecule #4: Small ribosomal subunit protein uS17
+Macromolecule #7: 60S ribosomal protein L8
+Macromolecule #8: 60S ribosomal protein L3
+Macromolecule #9: 60S ribosomal protein L4
+Macromolecule #10: 60S ribosomal protein L5
+Macromolecule #11: Large ribosomal subunit protein eL6
+Macromolecule #12: 60S ribosomal protein L7
+Macromolecule #13: Large ribosomal subunit protein eL8
+Macromolecule #14: Ribosomal protein L10
+Macromolecule #15: 60S ribosomal protein L13
+Macromolecule #16: 60S ribosomal protein L14
+Macromolecule #17: 60S ribosomal protein L15
+Macromolecule #18: Large ribosomal subunit protein uL13
+Macromolecule #19: 60S ribosomal protein L17
+Macromolecule #20: 60S ribosomal protein L19
+Macromolecule #21: Large ribosomal subunit protein eL20
+Macromolecule #22: 60S ribosomal protein L21
+Macromolecule #23: Large ribosomal subunit protein eL22
+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: eL41
+Macromolecule #41: eL42
+Macromolecule #42: 60S ribosomal protein L37a
+Macromolecule #43: 60S ribosomal protein L28
+Macromolecule #44: 40S ribosomal protein S3a
+Macromolecule #45: 40S ribosomal protein S13
+Macromolecule #46: 40S ribosomal protein S27
+Macromolecule #47: 60S acidic ribosomal protein P0
+Macromolecule #48: uL11
+Macromolecule #49: Proliferation-associated protein 2G4
+Macromolecule #50: Large ribosomal subunit protein eL18
+Macromolecule #51: 40S ribosomal protein S27a
+Macromolecule #52: 40S ribosomal protein S12
+Macromolecule #53: 40S ribosomal protein S25
+Macromolecule #54: Small ribosomal subunit protein uS7
+Macromolecule #55: 40S ribosomal protein S28
+Macromolecule #56: Small ribosomal subunit protein uS9
+Macromolecule #57: 40S ribosomal protein S10
+Macromolecule #58: Receptor of activated protein C kinase 1
+Macromolecule #59: 40S ribosomal protein S20
+Macromolecule #60: Small ribosomal subunit protein eS19
+Macromolecule #61: 40S ribosomal protein S18
+Macromolecule #62: 40S ribosomal protein S29
+Macromolecule #63: uS12
+Macromolecule #64: 40S ribosomal protein S24
+Macromolecule #65: 40S ribosomal protein S6
+Macromolecule #66: 40S ribosomal protein S4
+Macromolecule #67: 40S ribosomal protein S9
+Macromolecule #68: Small ribosomal subunit protein eS7
+Macromolecule #69: 40S ribosomal protein S30
+Macromolecule #70: Small ribosomal subunit protein uS3
+Macromolecule #71: 40S ribosomal protein S17
+Macromolecule #72: 40S ribosomal protein S15a
+Macromolecule #73: 40S ribosomal protein S8
+Macromolecule #74: Ribosomal protein L24
+Macromolecule #75: Small ribosomal subunit protein uS11
+Macromolecule #76: eS26
+Macromolecule #77: 60S ribosomal protein L11
+Macromolecule #78: 60S ribosomal protein L9
+Macromolecule #80: Elongation factor 2
+Macromolecule #81: La-related protein 1
+Macromolecule #82: Coiled-coil domain-containing protein 124
+Macromolecule #83: Small ribosomal subunit protein uS19
+Macromolecule #86: Ribosomal protein L23
+Macromolecule #5: 5.8S rRNA
+Macromolecule #6: 5S rRNA
+Macromolecule #79: 18S rRNA
+Macromolecule #84: ES27L
+Macromolecule #85: 28s rRNA
+Macromolecule #87: ZINC ION
+Macromolecule #88: GUANOSINE-5'-DIPHOSPHATE
-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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Image processing
-Atomic model buiding 1
| Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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| Refinement | Protocol: RIGID BODY FIT |
| Output model | ![]() PDB-11hg: |
-Atomic model buiding 2
| Refinement | Protocol: FLEXIBLE FIT |
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| Output model | ![]() PDB-11hg: |
Movie
Controller
About Yorodumi




Keywords
Authors
United States, 1 items
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