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Yorodumi- EMDB-38634: Cryo-EM structure of the human 55S mitoribosome with 10uM Tigecycline -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38634 | |||||||||
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Title | Cryo-EM structure of the human 55S mitoribosome with 10uM Tigecycline | |||||||||
Map data | refined map without post process | |||||||||
Sample |
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Keywords | ribosome / Tigecycline / antibiotic | |||||||||
Function / homology | Function and homology information mitochondrial ribosome binding / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation ...mitochondrial ribosome binding / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / negative regulation of mitotic nuclear division / peptidyl-tRNA hydrolase / mitochondrial ribosome / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial small ribosomal subunit / mitochondrial translation / aminoacyl-tRNA hydrolase activity / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / fibrillar center / double-stranded RNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit / cell junction / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / nuclear membrane / endonuclease activity / cell population proliferation / tRNA binding / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleotide binding / synapse / nucleolus / GTP binding / apoptotic process / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Li X / Wang M / Cheng J | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: 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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38634.map.gz | 225.3 MB | EMDB map data format | |
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Header (meta data) | emd-38634-v30.xml emd-38634.xml | 109.6 KB 109.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38634_fsc.xml | 14.9 KB | Display | FSC data file |
Images | emd_38634.png | 178.6 KB | ||
Filedesc metadata | emd-38634.cif.gz | 21.7 KB | ||
Others | emd_38634_additional_1.map.gz emd_38634_additional_2.map.gz emd_38634_half_map_1.map.gz emd_38634_half_map_2.map.gz | 161.5 MB 219.2 MB 226.1 MB 226.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38634 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38634 | HTTPS FTP |
-Validation report
Summary document | emd_38634_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_38634_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_38634_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | emd_38634_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38634 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38634 | HTTPS FTP |
-Related structure data
Related structure data | 8xt2MC 8k2aC 8k2bC 8k2cC 8k2dC 8k82C 8xsxC 8xsyC 8xszC 8xt0C 8xt1C 8xt3C 8yooC 8yopC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38634.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | refined map without post process | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: local resolution filtered map using Relion
File | emd_38634_additional_1.map | ||||||||||||
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Annotation | local resolution filtered map using Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: composite map from multibody refinement and filtered by DeepEMhancer
File | emd_38634_additional_2.map | ||||||||||||
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Annotation | composite map from multibody refinement and filtered by DeepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38634_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38634_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 55S ribosome with tigecycline
+Supramolecule #1: 55S ribosome with tigecycline
+Macromolecule #1: 16s rRNA
+Macromolecule #2: Val tRNA
+Macromolecule #83: 12s rRNA
+Macromolecule #3: Large ribosomal subunit protein uL2m
+Macromolecule #4: Large ribosomal subunit protein uL3m
+Macromolecule #5: Large ribosomal subunit protein uL4m
+Macromolecule #6: Large ribosomal subunit protein bL9m
+Macromolecule #7: Large ribosomal subunit protein uL10m
+Macromolecule #8: Large ribosomal subunit protein uL11m
+Macromolecule #9: Large ribosomal subunit protein uL13m
+Macromolecule #10: Large ribosomal subunit protein uL14m
+Macromolecule #11: Large ribosomal subunit protein uL15m
+Macromolecule #12: Large ribosomal subunit protein uL16m
+Macromolecule #13: Large ribosomal subunit protein bL17m
+Macromolecule #14: Mitochondrial ribosomal protein L18, isoform CRA_b
+Macromolecule #15: Large ribosomal subunit protein bL19m
+Macromolecule #16: Large ribosomal subunit protein bL20m
+Macromolecule #17: Large ribosomal subunit protein bL21m
+Macromolecule #18: 39S ribosomal protein L22, mitochondrial
+Macromolecule #19: Large ribosomal subunit protein uL23m
+Macromolecule #20: Large ribosomal subunit protein uL24m
+Macromolecule #21: Large ribosomal subunit protein bL27m
+Macromolecule #22: Large ribosomal subunit protein bL28m
+Macromolecule #23: Large ribosomal subunit protein uL29m
+Macromolecule #24: Large ribosomal subunit protein uL30m
+Macromolecule #25: Large ribosomal subunit protein bL32m
+Macromolecule #26: Large ribosomal subunit protein bL33m
+Macromolecule #27: Large ribosomal subunit protein bL34m
+Macromolecule #28: Large ribosomal subunit protein bL35m
+Macromolecule #29: Large ribosomal subunit protein bL36m
+Macromolecule #30: Large ribosomal subunit protein mL37
+Macromolecule #31: Large ribosomal subunit protein mL38
+Macromolecule #32: Large ribosomal subunit protein mL39
+Macromolecule #33: Large ribosomal subunit protein mL40
+Macromolecule #34: Large ribosomal subunit protein mL41
+Macromolecule #35: Large ribosomal subunit protein mL42
+Macromolecule #36: Large ribosomal subunit protein mL43
+Macromolecule #37: Large ribosomal subunit protein mL44
+Macromolecule #38: Large ribosomal subunit protein mL45
+Macromolecule #39: Large ribosomal subunit protein mL46
+Macromolecule #40: Large ribosomal subunit protein mL48
+Macromolecule #41: Large ribosomal subunit protein mL49
+Macromolecule #42: Large ribosomal subunit protein mL50
+Macromolecule #43: Large ribosomal subunit protein mL51
+Macromolecule #44: 39S ribosomal protein L52, mitochondrial
+Macromolecule #45: Large ribosomal subunit protein mL53
+Macromolecule #46: Large ribosomal subunit protein mL54
+Macromolecule #47: Large ribosomal subunit protein mL55
+Macromolecule #48: Large ribosomal subunit protein mL63
+Macromolecule #49: Large ribosomal subunit protein mL62
+Macromolecule #50: Large ribosomal subunit protein mL64
+Macromolecule #51: Large ribosomal subunit protein mL66
+Macromolecule #52: Large ribosomal subunit protein mL65
+Macromolecule #53: Small ribosomal subunit protein uS2m
+Macromolecule #54: Small ribosomal subunit protein uS3m
+Macromolecule #55: Small ribosomal subunit protein uS5m
+Macromolecule #56: Small ribosomal subunit protein bS6m
+Macromolecule #57: Small ribosomal subunit protein uS7m
+Macromolecule #58: Small ribosomal subunit protein uS9m
+Macromolecule #59: Small ribosomal subunit protein uS10m
+Macromolecule #60: Small ribosomal subunit protein uS11m
+Macromolecule #61: Small ribosomal subunit protein uS12m
+Macromolecule #62: Small ribosomal subunit protein uS14m
+Macromolecule #63: Small ribosomal subunit protein uS15m
+Macromolecule #64: Small ribosomal subunit protein bS16m
+Macromolecule #65: Small ribosomal subunit protein uS17m
+Macromolecule #66: Small ribosomal subunit protein mS40
+Macromolecule #67: Small ribosomal subunit protein bS18m
+Macromolecule #68: Small ribosomal subunit protein bS21m
+Macromolecule #69: Small ribosomal subunit protein mS22
+Macromolecule #70: Small ribosomal subunit protein mS23
+Macromolecule #71: Small ribosomal subunit protein mS25
+Macromolecule #72: Small ribosomal subunit protein mS26
+Macromolecule #73: Small ribosomal subunit protein mS27
+Macromolecule #74: Small ribosomal subunit protein bS1m
+Macromolecule #75: Small ribosomal subunit protein mS29
+Macromolecule #76: Small ribosomal subunit protein mS31
+Macromolecule #77: Small ribosomal subunit protein mS33
+Macromolecule #78: Small ribosomal subunit protein mS34
+Macromolecule #79: Small ribosomal subunit protein mS35
+Macromolecule #80: Small ribosomal subunit protein mS37
+Macromolecule #81: Small ribosomal subunit protein mS38
+Macromolecule #82: Small ribosomal subunit protein mS39
+Macromolecule #84: MAGNESIUM ION
+Macromolecule #85: TIGECYCLINE
+Macromolecule #86: ZINC ION
+Macromolecule #87: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k 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: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |