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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | human mitoribosome trapped by retapamulin | |||||||||
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Sample |
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Keywords | mitoribosome / retapamulin / RIBOSOME | |||||||||
| Function / homology | Function and homology informationrRNA import into mitochondrion / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / translation release factor activity ...rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / translation release factor activity / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial ribosome / mitochondrial small ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase activity / mitochondrial translation / apoptotic mitochondrial changes / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled cytosolic ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / fibrillar center / cell junction / double-stranded RNA binding / regulation of translation / ribosomal small subunit assembly / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / cell population proliferation / negative regulation of translation / mitochondrial inner membrane / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / intracellular membrane-bounded organelle / mRNA binding / apoptotic process / positive regulation of DNA-templated transcription / GTP binding / nucleolus / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Ando Y / Nureki O / Itoh Y | |||||||||
| Funding support | Japan, 2 items
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Citation | Journal: Mol Cell / Year: 2025Title: Monitoring the complexity and dynamics of mitochondrial translation. Authors: Taisei Wakigawa / Mari Mito / Yushin Ando / Haruna Yamashiro / Kotaro Tomuro / Haruna Tani / Kazuhito Tomizawa / Takeshi Chujo / Asuteka Nagao / Takeo Suzuki / Osamu Nureki / Fan-Yan Wei / ...Authors: Taisei Wakigawa / Mari Mito / Yushin Ando / Haruna Yamashiro / Kotaro Tomuro / Haruna Tani / Kazuhito Tomizawa / Takeshi Chujo / Asuteka Nagao / Takeo Suzuki / Osamu Nureki / Fan-Yan Wei / Yuichi Shichino / Yuzuru Itoh / Tsutomu Suzuki / Shintaro Iwasaki / ![]() Abstract: Since mitochondrial translation leads to the synthesis of the essential oxidative phosphorylation (OXPHOS) subunits, exhaustive and quantitative delineation of mitoribosome traversal is needed. Here, ...Since mitochondrial translation leads to the synthesis of the essential oxidative phosphorylation (OXPHOS) subunits, exhaustive and quantitative delineation of mitoribosome traversal is needed. Here, we developed a variety of high-resolution mitochondrial ribosome profiling derivatives and revealed the intricate regulation of mammalian mitochondrial translation. Harnessing a translation inhibitor, retapamulin, our approach assessed the stoichiometry and kinetics of mitochondrial translation flux, such as the number of mitoribosomes on a transcript, the elongation rate, and the initiation rate. We also surveyed the impacts of modifications at the anticodon stem loop in mitochondrial tRNAs (mt-tRNAs), including all possible modifications at the 34th position, in cells deleting the corresponding enzymes and derived from patients, as well as in mouse tissues. Moreover, a retapamulin-assisted derivative and mito-disome profiling revealed mitochondrial translation initiation factor (mtIF) 3-mediated translation initiation from internal open reading frames (ORFs) and programmed mitoribosome collision sites across the mitochondrial transcriptome. Our work provides a useful platform for investigating protein synthesis within the energy powerhouse of the cell. | |||||||||
| History |
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_64554.map.gz | 256 MB | EMDB map data format | |
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| Header (meta data) | emd-64554-v30.xml emd-64554.xml | 108.6 KB 108.6 KB | Display Display | EMDB header |
| Images | emd_64554.png | 186.5 KB | ||
| Filedesc metadata | emd-64554.cif.gz | 22.9 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-64554 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-64554 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9uwhMC C: citing same article ( M: atomic model generated by this map |
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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_64554.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| 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
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Sample components
+Entire : human mitoribosome trapped by retapamulin
+Supramolecule #1: human mitoribosome trapped by retapamulin
+Macromolecule #1: 16S mitochondrial rRNA
+Macromolecule #2: mitochondrial tRNAVal
+Macromolecule #25: 12S mitochondrial rRNA
+Macromolecule #56: P/P-tRNA
+Macromolecule #57: mRNA
+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: Large ribosomal subunit protein uL18m
+Macromolecule #15: Large ribosomal subunit protein bL19m
+Macromolecule #16: Large ribosomal subunit protein bL20m
+Macromolecule #17: Large ribosomal subunit protein bL21m
+Macromolecule #18: Large ribosomal subunit protein uL22m
+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 #26: Small ribosomal subunit protein uS2m
+Macromolecule #27: Small ribosomal subunit protein uS3m
+Macromolecule #28: Small ribosomal subunit protein uS5m
+Macromolecule #29: Small ribosomal subunit protein bS6m
+Macromolecule #30: Small ribosomal subunit protein uS7m
+Macromolecule #31: Small ribosomal subunit protein uS9m
+Macromolecule #32: Small ribosomal subunit protein uS10m
+Macromolecule #33: Small ribosomal subunit protein uS11m
+Macromolecule #34: Small ribosomal subunit protein uS12m
+Macromolecule #35: Small ribosomal subunit protein uS14m
+Macromolecule #36: Small ribosomal subunit protein uS15m
+Macromolecule #37: Small ribosomal subunit protein bS16m
+Macromolecule #38: Small ribosomal subunit protein uS17m
+Macromolecule #39: Small ribosomal subunit protein mS40
+Macromolecule #40: Small ribosomal subunit protein bS18m
+Macromolecule #41: MRPS21 isoform 1
+Macromolecule #42: Small ribosomal subunit protein mS22
+Macromolecule #43: Small ribosomal subunit protein mS23
+Macromolecule #44: Small ribosomal subunit protein mS25
+Macromolecule #45: Small ribosomal subunit protein mS26
+Macromolecule #46: Small ribosomal subunit protein mS27
+Macromolecule #47: Small ribosomal subunit protein bS1m
+Macromolecule #48: Small ribosomal subunit protein mS29
+Macromolecule #49: Small ribosomal subunit protein mS31
+Macromolecule #50: Small ribosomal subunit protein mS33
+Macromolecule #51: Small ribosomal subunit protein mS34
+Macromolecule #52: Small ribosomal subunit protein mS35
+Macromolecule #53: Small ribosomal subunit protein mS37
+Macromolecule #54: Small ribosomal subunit protein mS38
+Macromolecule #55: Small ribosomal subunit protein mS39
+Macromolecule #58: Large ribosomal subunit protein bL32m
+Macromolecule #59: Large ribosomal subunit protein bL33m
+Macromolecule #60: Large ribosomal subunit protein bL34m
+Macromolecule #61: Large ribosomal subunit protein bL35m
+Macromolecule #62: Large ribosomal subunit protein bL36m
+Macromolecule #63: Large ribosomal subunit protein mL37
+Macromolecule #64: Large ribosomal subunit protein mL38
+Macromolecule #65: Large ribosomal subunit protein mL39
+Macromolecule #66: Large ribosomal subunit protein mL40
+Macromolecule #67: Large ribosomal subunit protein mL41
+Macromolecule #68: Large ribosomal subunit protein mL42
+Macromolecule #69: Large ribosomal subunit protein mL43
+Macromolecule #70: Large ribosomal subunit protein mL44
+Macromolecule #71: Large ribosomal subunit protein mL45
+Macromolecule #72: Large ribosomal subunit protein mL46
+Macromolecule #73: Large ribosomal subunit protein mL48
+Macromolecule #74: Large ribosomal subunit protein mL49
+Macromolecule #75: Large ribosomal subunit protein mL50
+Macromolecule #76: Large ribosomal subunit protein mL51
+Macromolecule #77: Large ribosomal subunit protein mL52
+Macromolecule #78: Large ribosomal subunit protein mL53
+Macromolecule #79: Large ribosomal subunit protein mL54
+Macromolecule #80: Large ribosomal subunit protein mL55
+Macromolecule #81: Large ribosomal subunit protein mL63
+Macromolecule #82: Large ribosomal subunit protein mL62
+Macromolecule #83: Large ribosomal subunit protein mL64
+Macromolecule #84: Large ribosomal subunit protein mL66
+Macromolecule #85: Large ribosomal subunit protein mL65
+Macromolecule #86: Large ribosomal subunit protein bL12m
+Macromolecule #87: MAGNESIUM ION
+Macromolecule #88: POTASSIUM ION
+Macromolecule #89: Retapamulin
+Macromolecule #90: VALINE
+Macromolecule #91: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #92: SPERMIDINE
+Macromolecule #93: ZINC ION
+Macromolecule #94: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #95: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #96: 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: 7.5 |
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| Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 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: 1.6 µm / Nominal defocus min: 0.8 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Homo sapiens (human)
Authors
Japan, 2 items
Citation





















Z (Sec.)
Y (Row.)
X (Col.)



























Processing
FIELD EMISSION GUN

