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Yorodumi- EMDB-38660: State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 t... -
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Basic information
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| Title | State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation | ||||||||||||
Map data | A_P_rotated_80S ribosome | ||||||||||||
Sample |
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Keywords | 80S / compact eEF2 / elongation cycle / rotated / TRANSLATION | ||||||||||||
| Function / homology | Function and homology informationPeptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / Protein methylation ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of translational frameshifting / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / positive regulation of protein kinase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / translation elongation factor activity / regulation of translational fidelity / protein-RNA complex assembly / translational termination / ribosomal subunit export from nucleus / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / rescue of stalled ribosome / protein kinase C binding / cellular response to amino acid starvation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA / macroautophagy / small-subunit processome / translational initiation / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / protein-folding chaperone binding / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / ribonucleoprotein complex / negative regulation of gene expression / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding Similarity search - Function | ||||||||||||
| Biological species | ![]() | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Cheng J / Wu CL / Li JX / Zhang XZ | ||||||||||||
| Funding support | China, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2025Title: Capturing eukaryotic ribosome dynamics in situ at high resolution. Authors: Jing Cheng / Chunling Wu / Junxi Li / Qi Yang / Mingjie Zhao / Xinzheng Zhang / ![]() Abstract: Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ...Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ribosome particles from Saccharomyces cerevisiae cell lamellae were obtained to solve the 60S region to 2.9-Å resolution by in situ single-particle analysis. Over 20 distinct conformations were identified by three-dimensional classification with resolutions typically higher than 4 Å. These conformations were used to reconstruct a complete elongation cycle of eukaryotic translation with elongation factors (eEFs). We found that compact eEF2 anchors to the partially rotated ribosome after subunit rolling and hypothesize that it stabilizes the local conformation for peptidyl transfer. Moreover, open-eEF3 binding to a fully rotated ribosome was observed, whose conformational change was coupled with head swiveling and body back-rotation of the 40S subunit. | ||||||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_38660.map.gz | 230 MB | EMDB map data format | |
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| Header (meta data) | emd-38660-v30.xml emd-38660.xml | 100.8 KB 100.8 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_38660_fsc.xml | 14.8 KB | Display | FSC data file |
| Images | emd_38660.png | 119.9 KB | ||
| Masks | emd_38660_msk_1.map | 244.1 MB | Mask map | |
| Filedesc metadata | emd-38660.cif.gz | 18.7 KB | ||
| Others | emd_38660_half_map_1.map.gz emd_38660_half_map_2.map.gz | 226.4 MB 226.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38660 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38660 | HTTPS FTP |
-Validation report
| Summary document | emd_38660_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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| Full document | emd_38660_full_validation.pdf.gz | 1.3 MB | Display | |
| Data in XML | emd_38660_validation.xml.gz | 22.5 KB | Display | |
| Data in CIF | emd_38660_validation.cif.gz | 29.2 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38660 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38660 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8xu8MC ![]() 8yldC ![]() 8ylrC ![]() 8z70C ![]() 8z71C 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_38660.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | A_P_rotated_80S ribosome | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_38660_msk_1.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
-Half map: half map
| File | emd_38660_half_map_1.map | ||||||||||||
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| Annotation | half_map | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: half map
| File | emd_38660_half_map_2.map | ||||||||||||
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| Annotation | half_map | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : Yeast 80S ribosome with compact eEF2 and tRNAs
+Supramolecule #1: Yeast 80S ribosome with compact eEF2 and tRNAs
+Macromolecule #1: 18S rRNA
+Macromolecule #2: 25S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: 5.8S rRNA
+Macromolecule #46: tRNA
+Macromolecule #5: Large ribosomal subunit protein uL2A
+Macromolecule #6: Large ribosomal subunit protein uL3
+Macromolecule #7: Large ribosomal subunit protein uL4A
+Macromolecule #8: Large ribosomal subunit protein uL18
+Macromolecule #9: Large ribosomal subunit protein eL6B
+Macromolecule #10: Large ribosomal subunit protein uL30A
+Macromolecule #11: Large ribosomal subunit protein eL8A
+Macromolecule #12: Large ribosomal subunit protein uL6A
+Macromolecule #13: Large ribosomal subunit protein uL16
+Macromolecule #14: Large ribosomal subunit protein uL5B
+Macromolecule #15: Large ribosomal subunit protein eL13A
+Macromolecule #16: Large ribosomal subunit protein eL14A
+Macromolecule #17: Large ribosomal subunit protein eL15A
+Macromolecule #18: Large ribosomal subunit protein uL13A
+Macromolecule #19: Large ribosomal subunit protein uL22A
+Macromolecule #20: Large ribosomal subunit protein eL18A
+Macromolecule #21: Large ribosomal subunit protein eL19A
+Macromolecule #22: Large ribosomal subunit protein eL20A
+Macromolecule #23: Large ribosomal subunit protein eL21A
+Macromolecule #24: Large ribosomal subunit protein eL22A
+Macromolecule #25: Large ribosomal subunit protein uL14A
+Macromolecule #26: Large ribosomal subunit protein eL24A
+Macromolecule #27: Large ribosomal subunit protein uL23
+Macromolecule #28: Large ribosomal subunit protein uL24A
+Macromolecule #29: Large ribosomal subunit protein eL27A
+Macromolecule #30: Large ribosomal subunit protein uL15
+Macromolecule #31: Large ribosomal subunit protein eL29
+Macromolecule #32: Large ribosomal subunit protein eL30
+Macromolecule #33: Large ribosomal subunit protein eL31A
+Macromolecule #34: Large ribosomal subunit protein eL32
+Macromolecule #35: Large ribosomal subunit protein eL33A
+Macromolecule #36: Large ribosomal subunit protein eL34A
+Macromolecule #37: Large ribosomal subunit protein uL29A
+Macromolecule #38: Large ribosomal subunit protein eL36A
+Macromolecule #39: Large ribosomal subunit protein eL37A
+Macromolecule #40: Large ribosomal subunit protein eL38
+Macromolecule #41: Large ribosomal subunit protein eL39
+Macromolecule #42: Large ribosomal subunit protein eL40A
+Macromolecule #43: Large ribosomal subunit protein eL41A
+Macromolecule #44: Large ribosomal subunit protein eL42A
+Macromolecule #45: Large ribosomal subunit protein eL43A
+Macromolecule #47: Elongation factor 2
+Macromolecule #48: Small ribosomal subunit protein eS12
+Macromolecule #49: Small ribosomal subunit protein uS11B
+Macromolecule #50: Small ribosomal subunit protein eS26A
+Macromolecule #51: Small ribosomal subunit protein eS10A
+Macromolecule #52: Small ribosomal subunit protein uS19
+Macromolecule #53: Small ribosomal subunit protein uS3
+Macromolecule #54: Small ribosomal subunit protein eS19A
+Macromolecule #55: Small ribosomal subunit protein uS10
+Macromolecule #56: Small ribosomal subunit protein eS28A
+Macromolecule #57: Small ribosomal subunit protein uS14A
+Macromolecule #58: Small ribosomal subunit protein uS7
+Macromolecule #59: Small ribosomal subunit protein uS9A
+Macromolecule #60: Small ribosomal subunit protein uS13A
+Macromolecule #61: Small ribosomal subunit protein RACK1
+Macromolecule #62: Small ribosomal subunit protein eS31
+Macromolecule #63: Small ribosomal subunit protein eS17A
+Macromolecule #64: Small ribosomal subunit protein uS2A
+Macromolecule #65: Small ribosomal subunit protein eS1A
+Macromolecule #66: Small ribosomal subunit protein uS5
+Macromolecule #67: Small ribosomal subunit protein eS4A
+Macromolecule #68: Small ribosomal subunit protein eS6A
+Macromolecule #69: Small ribosomal subunit protein eS7A
+Macromolecule #70: Small ribosomal subunit protein eS8A
+Macromolecule #71: Small ribosomal subunit protein uS4A
+Macromolecule #72: Small ribosomal subunit protein uS17A
+Macromolecule #73: Small ribosomal subunit protein uS15
+Macromolecule #74: Small ribosomal subunit protein eS21A
+Macromolecule #75: Small ribosomal subunit protein uS8A
+Macromolecule #76: Small ribosomal subunit protein uS12A
+Macromolecule #77: Small ribosomal subunit protein eS24A
+Macromolecule #78: Small ribosomal subunit protein eS27A
+Macromolecule #79: Small ribosomal subunit protein eS30A
+Macromolecule #80: Small ribosomal subunit protein eS25A
-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: 4.5 / Details: YPD |
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| Grid | Material: COPPER |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: GATAN K2 QUANTUM (4k 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: 3.0 µm / Nominal defocus min: 0.8 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Authors
China, 3 items
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Processing
FIELD EMISSION GUN

