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Yorodumi- EMDB-36839: Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF... -
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Basic information
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| Title | Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A | |||||||||
Map data | DeepEMhancer | |||||||||
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Keywords | 80S ribosome / tigecycline / antibiotic / RIBOSOME | |||||||||
| Function / homology | Function and homology informationcytoplasmic translational elongation through polyproline stretches / positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / cytoplasmic translational elongation / positive regulation of translational termination / Peptide chain elongation / Synthesis of diphthamide-EEF2 / triplex DNA binding ...cytoplasmic translational elongation through polyproline stretches / positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / cytoplasmic translational elongation / positive regulation of translational termination / Peptide chain elongation / Synthesis of diphthamide-EEF2 / triplex DNA binding / cytoplasmic translational termination / ribosome hibernation / translation elongation factor binding / Platelet degranulation / positive regulation of translational elongation / regulation of translational initiation in response to stress / 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 / telomeric DNA binding / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of translational frameshifting / SRP-dependent cotranslational protein targeting to membrane / TOR signaling / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / 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) / Formation of a pool of free 40S subunits / positive regulation of translational initiation / 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 / 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) / ribosomal small subunit export from nucleus / translation regulator activity / translation repressor activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / translation initiation factor activity / Neutrophil degranulation / rescue of stalled ribosome / telomere maintenance / 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 Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Buschauer R / Beckmann R / Cheng J | |||||||||
| Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2024Title: Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline. Authors: Xiang Li / Mengjiao Wang / Timo Denk / Robert Buschauer / Yi Li / Roland Beckmann / Jingdong Cheng / ![]() Abstract: Tigecycline is widely used for treating complicated bacterial infections for which there are no effective drugs. It inhibits bacterial protein translation by blocking the ribosomal A-site. However, ...Tigecycline is widely used for treating complicated bacterial infections for which there are no effective drugs. It inhibits bacterial protein translation by blocking the ribosomal A-site. However, even though it is also cytotoxic for human cells, the molecular mechanism of its inhibition remains unclear. Here, we present cryo-EM structures of tigecycline-bound human mitochondrial 55S, 39S, cytoplasmic 80S and yeast cytoplasmic 80S ribosomes. We find that at clinically relevant concentrations, tigecycline effectively targets human 55S mitoribosomes, potentially, by hindering A-site tRNA accommodation and by blocking the peptidyl transfer center. In contrast, tigecycline does not bind to human 80S ribosomes under physiological concentrations. However, at high tigecycline concentrations, in addition to blocking the A-site, both human and yeast 80S ribosomes bind tigecycline at another conserved binding site restricting the movement of the L1 stalk. In conclusion, the observed distinct binding properties of tigecycline may guide new pathways for drug design and therapy. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_36839.map.gz | 372.8 MB | EMDB map data format | |
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| Header (meta data) | emd-36839-v30.xml emd-36839.xml | 107.8 KB 107.8 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_36839_fsc.xml | 17.1 KB | Display | FSC data file |
| Images | emd_36839.png | 116.8 KB | ||
| Filedesc metadata | emd-36839.cif.gz | 19.7 KB | ||
| Others | emd_36839_additional_1.map.gz emd_36839_additional_2.map.gz emd_36839_half_map_1.map.gz emd_36839_half_map_2.map.gz | 336.8 MB 244.4 MB 337.8 MB 338.1 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36839 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36839 | HTTPS FTP |
-Validation report
| Summary document | emd_36839_validation.pdf.gz | 928.2 KB | Display | EMDB validaton report |
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| Full document | emd_36839_full_validation.pdf.gz | 927.8 KB | Display | |
| Data in XML | emd_36839_validation.xml.gz | 25.1 KB | Display | |
| Data in CIF | emd_36839_validation.cif.gz | 33.2 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36839 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36839 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8k2dMC ![]() 8k2aC ![]() 8k2bC ![]() 8k2cC ![]() 8k82C ![]() 8xsxC ![]() 8xsyC ![]() 8xszC ![]() 8xt0C ![]() 8xt1C ![]() 8xt2C ![]() 8xt3C ![]() 8yooC ![]() 8yopC 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_36839.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | DeepEMhancer | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.847 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: consensus map
| File | emd_36839_additional_1.map | ||||||||||||
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| Annotation | consensus map | ||||||||||||
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| Density Histograms |
-Additional map: local filter
| File | emd_36839_additional_2.map | ||||||||||||
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| Annotation | local filter | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_36839_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #2
| File | emd_36839_half_map_2.map | ||||||||||||
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Sample components
+Entire : yeast 80S ribosome
+Supramolecule #1: yeast 80S ribosome
+Macromolecule #1: 18S rRNA
+Macromolecule #2: 23S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: 5.8S rRNA
+Macromolecule #5: Small ribosomal subunit protein uS2A
+Macromolecule #6: 40S ribosomal protein S1-A
+Macromolecule #7: 40S ribosomal protein S2
+Macromolecule #8: Small ribosomal subunit protein uS3
+Macromolecule #9: 40S ribosomal protein S4-A
+Macromolecule #10: Small ribosomal subunit protein uS7
+Macromolecule #11: 40S ribosomal protein S6-A
+Macromolecule #12: 40S ribosomal protein S7-A
+Macromolecule #13: 40S ribosomal protein S8-A
+Macromolecule #14: 40S ribosomal protein S9-A
+Macromolecule #15: Small ribosomal subunit protein eS10A
+Macromolecule #16: Small ribosomal subunit protein uS17A
+Macromolecule #17: Small ribosomal subunit protein eS12
+Macromolecule #18: 40S ribosomal protein S13
+Macromolecule #19: 40S ribosomal protein S14-A
+Macromolecule #20: Small ribosomal subunit protein uS19
+Macromolecule #21: Small ribosomal subunit protein uS9A
+Macromolecule #22: Small ribosomal subunit protein eS17A
+Macromolecule #23: Small ribosomal subunit protein uS13A
+Macromolecule #24: Small ribosomal subunit protein eS19A
+Macromolecule #25: Small ribosomal subunit protein uS10
+Macromolecule #26: Small ribosomal subunit protein eS21A
+Macromolecule #27: 40S ribosomal protein S22-A
+Macromolecule #28: 40S ribosomal protein S23-A
+Macromolecule #29: 40S ribosomal protein S24-A
+Macromolecule #30: Small ribosomal subunit protein eS25A
+Macromolecule #31: Small ribosomal subunit protein eS26B
+Macromolecule #32: 40S ribosomal protein S27-A
+Macromolecule #33: Small ribosomal subunit protein eS28A
+Macromolecule #34: Small ribosomal subunit protein uS14A
+Macromolecule #35: 40S ribosomal protein S30-A
+Macromolecule #36: Ubiquitin-ribosomal protein eS31 fusion protein
+Macromolecule #37: Small ribosomal subunit protein RACK1
+Macromolecule #38: Large ribosomal subunit protein uL2A
+Macromolecule #39: Large ribosomal subunit protein uL3
+Macromolecule #40: Large ribosomal subunit protein uL4A
+Macromolecule #41: Large ribosomal subunit protein uL18
+Macromolecule #42: Large ribosomal subunit protein eL6A
+Macromolecule #43: Large ribosomal subunit protein uL30A
+Macromolecule #44: Large ribosomal subunit protein eL8A
+Macromolecule #45: Large ribosomal subunit protein uL6A
+Macromolecule #46: Large ribosomal subunit protein uL16
+Macromolecule #47: Large ribosomal subunit protein uL5A
+Macromolecule #48: Large ribosomal subunit protein uL11A
+Macromolecule #49: Large ribosomal subunit protein eL13A
+Macromolecule #50: Large ribosomal subunit protein eL14A
+Macromolecule #51: Large ribosomal subunit protein eL15A
+Macromolecule #52: Large ribosomal subunit protein uL13A
+Macromolecule #53: Large ribosomal subunit protein uL22A
+Macromolecule #54: Large ribosomal subunit protein eL18A
+Macromolecule #55: Large ribosomal subunit protein eL19A
+Macromolecule #56: Large ribosomal subunit protein eL20A
+Macromolecule #57: Large ribosomal subunit protein eL21A
+Macromolecule #58: Large ribosomal subunit protein eL22A
+Macromolecule #59: Large ribosomal subunit protein uL14A
+Macromolecule #60: Large ribosomal subunit protein eL24A
+Macromolecule #61: Large ribosomal subunit protein uL23
+Macromolecule #62: Large ribosomal subunit protein uL24A
+Macromolecule #63: Large ribosomal subunit protein eL27A
+Macromolecule #64: Large ribosomal subunit protein uL15
+Macromolecule #65: Large ribosomal subunit protein eL29
+Macromolecule #66: Large ribosomal subunit protein eL30
+Macromolecule #67: Large ribosomal subunit protein eL31A
+Macromolecule #68: Large ribosomal subunit protein eL32
+Macromolecule #69: Large ribosomal subunit protein eL33A
+Macromolecule #70: Large ribosomal subunit protein eL34A
+Macromolecule #71: Large ribosomal subunit protein uL29A
+Macromolecule #72: Large ribosomal subunit protein eL36A
+Macromolecule #73: Large ribosomal subunit protein eL37A
+Macromolecule #74: Large ribosomal subunit protein eL38
+Macromolecule #75: Large ribosomal subunit protein eL39
+Macromolecule #76: Ubiquitin-ribosomal protein eL40A fusion protein
+Macromolecule #77: Large ribosomal subunit protein eL41A
+Macromolecule #78: Large ribosomal subunit protein eL42A
+Macromolecule #79: Large ribosomal subunit protein eL43A
+Macromolecule #80: Eukaryotic translation initiation factor 5A-1
+Macromolecule #81: Large ribosomal subunit protein uL1A
+Macromolecule #82: Large ribosomal subunit protein uL10
+Macromolecule #83: Elongation factor 2
+Macromolecule #84: Suppressor protein STM1
+Macromolecule #85: ZINC ION
+Macromolecule #86: TIGECYCLINE
+Macromolecule #87: MAGNESIUM ION
+Macromolecule #88: GUANOSINE-5'-DIPHOSPHATE
-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: 7.4 |
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| 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 K2 SUMMIT (4k x 4k) / Average electron dose: 44.0 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: 3.5 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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FIELD EMISSION GUN

