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Yorodumi- EMDB-52283: Translational activator Aep3 in complex with mRNA and the yeast m... -
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Open data
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Basic information
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| Title | Translational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome | |||||||||
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Keywords | Mitoribosome / translation / RIBOSOME | |||||||||
| Function / homology | Function and homology informationBranched-chain amino acid catabolism / positive regulation of mitochondrial DNA replication / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mRNA metabolic process / mitochondrial translational initiation / L-valine catabolic process / mitochondrial respiratory chain complex IV assembly / Mitochondrial protein degradation / mitochondrial ribosome assembly ...Branched-chain amino acid catabolism / positive regulation of mitochondrial DNA replication / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mRNA metabolic process / mitochondrial translational initiation / L-valine catabolic process / mitochondrial respiratory chain complex IV assembly / Mitochondrial protein degradation / mitochondrial ribosome assembly / DNA strand exchange activity / ribonuclease III activity / : / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / sporulation resulting in formation of a cellular spore / superoxide dismutase activity / RNA processing / cell redox homeostasis / mRNA processing / peroxisome / single-stranded DNA binding / double-stranded RNA binding / large ribosomal subunit / ribosome biogenesis / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cellular response to oxidative stress / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / DNA recombination / cytosolic large ribosomal subunit / negative regulation of translation / mitochondrial inner membrane / rRNA binding / structural constituent of ribosome / ribosome / translation / mRNA binding / regulation of DNA-templated transcription / GTP binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
| Biological species | ![]() ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Carlstrom A / Rovsnik U / Ott M | |||||||||
| Funding support | Sweden, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2025Title: Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation. Authors: Joseph B Bridgers / Andreas Carlström / Dawafuti Sherpa / Mary T Couvillion / Urška Rovšnik / Jingjing Gao / Bowen Wan / Sichen Shao / Martin Ott / L Stirling Churchman / ![]() Abstract: Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains ...Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains elusive. In Saccharomyces cerevisiae, nuclear-encoded mitochondrial translational activators (TAs) facilitate transcript-specific translation by a yet unknown mechanism. Here, we investigated the function of TAs containing RNA-binding pentatricopeptide repeats using selective mitoribosome profiling and cryo-electron microscopy (cryo-EM) structural analysis. These analyses show that TAs exhibit strong selectivity for mitoribosomes initiating on their target transcripts. Moreover, TA-mitoribosome footprints indicate that TAs recruit mitoribosomes proximal to the start codon. Two cryo-EM structures of mRNA-TA complexes bound to mitoribosomes stalled in the post-initiation, pre-elongation state revealed the general mechanism of TA action. Specifically, the TAs bind to structural elements in the 5' untranslated region of the client mRNA and the mRNA channel exit to align the mRNA in the small subunit during initiation. Our findings provide a mechanistic basis for understanding how mitochondria achieve transcript-specific translation initiation without relying on general sequence elements to position mitoribosomes at start codons. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_52283.map.gz | 455.7 MB | EMDB map data format | |
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| Header (meta data) | emd-52283-v30.xml emd-52283.xml | 114.8 KB 114.8 KB | Display Display | EMDB header |
| Images | emd_52283.png | 59.4 KB | ||
| Filedesc metadata | emd-52283.cif.gz | 22.4 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-52283 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-52283 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9hm0MC ![]() 9hlzC 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_52283.map.gz / Format: CCP4 / Size: 1000 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: 0.828 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 : Aep3 in complex with the 74S mitochondrial ribosome
+Supramolecule #1: Aep3 in complex with the 74S mitochondrial ribosome
+Supramolecule #2: 37S mitochondrial ribosome small subunit
+Supramolecule #3: 54S mitochondrial ribosome large subunit
+Macromolecule #1: Small ribosomal subunit protein mS38
+Macromolecule #2: Small ribosomal subunit protein mS41
+Macromolecule #3: Small ribosomal subunit protein mS42
+Macromolecule #4: Small ribosomal subunit protein mS43
+Macromolecule #5: Small ribosomal subunit protein mS27
+Macromolecule #6: Small ribosomal subunit protein mS45
+Macromolecule #7: Small ribosomal subunit protein mS46
+Macromolecule #8: Small ribosomal subunit protein mS47
+Macromolecule #9: Small ribosomal subunit protein bS1m
+Macromolecule #10: Small ribosomal subunit protein uS2m
+Macromolecule #11: Small ribosomal subunit protein uS3m
+Macromolecule #12: Small ribosomal subunit protein uS4m
+Macromolecule #13: Small ribosomal subunit protein uS5m
+Macromolecule #14: Small ribosomal subunit protein bS6m
+Macromolecule #15: Small ribosomal subunit protein uS7m
+Macromolecule #16: Small ribosomal subunit protein uS8m
+Macromolecule #17: Small ribosomal subunit protein uS9m
+Macromolecule #18: Small ribosomal subunit protein uS10m
+Macromolecule #19: Small ribosomal subunit protein uS11m
+Macromolecule #20: Small ribosomal subunit protein uS12m
+Macromolecule #21: Small ribosomal subunit protein uS13m
+Macromolecule #22: Small ribosomal subunit protein uS14m
+Macromolecule #23: Small ribosomal subunit protein uS15m
+Macromolecule #24: Small ribosomal subunit protein bS16m
+Macromolecule #25: Small ribosomal subunit protein uS17m
+Macromolecule #26: Small ribosomal subunit protein bS18m
+Macromolecule #27: Small ribosomal subunit protein uS19m
+Macromolecule #28: Small ribosomal subunit protein bS21m
+Macromolecule #29: Small ribosomal subunit protein mS23
+Macromolecule #30: Small ribosomal subunit protein mS29
+Macromolecule #31: Small ribosomal subunit protein mS33
+Macromolecule #32: Small ribosomal subunit protein mS35
+Macromolecule #33: Small ribosomal subunit protein mS37
+Macromolecule #34: ATPase expression protein 3
+Macromolecule #36: Large ribosomal subunit protein bL36m
+Macromolecule #37: Large ribosomal subunit protein mL38
+Macromolecule #38: Large ribosomal subunit protein mL40
+Macromolecule #39: Large ribosomal subunit protein mL41
+Macromolecule #40: Large ribosomal subunit protein mL43
+Macromolecule #41: Large ribosomal subunit protein mL44
+Macromolecule #42: Large ribosomal subunit protein mL46
+Macromolecule #43: Large ribosomal subunit protein mL49
+Macromolecule #44: Large ribosomal subunit protein mL50
+Macromolecule #45: Large ribosomal subunit protein mL57
+Macromolecule #47: Large ribosomal subunit protein uL2m
+Macromolecule #48: Large ribosomal subunit protein uL3m
+Macromolecule #49: Large ribosomal subunit protein uL4m
+Macromolecule #50: Large ribosomal subunit protein uL5m
+Macromolecule #51: Large ribosomal subunit protein uL6m
+Macromolecule #52: Large ribosomal subunit protein bL9m
+Macromolecule #53: Large ribosomal subunit protein uL13m
+Macromolecule #54: Large ribosomal subunit protein uL14m
+Macromolecule #55: Large ribosomal subunit protein uL15m
+Macromolecule #56: Large ribosomal subunit protein uL16m
+Macromolecule #57: Large ribosomal subunit protein bL17m
+Macromolecule #58: Large ribosomal subunit protein bL19m
+Macromolecule #59: Large ribosomal subunit protein bL21m
+Macromolecule #60: Large ribosomal subunit protein uL22m
+Macromolecule #61: Large ribosomal subunit protein uL23m
+Macromolecule #62: Large ribosomal subunit protein uL24m
+Macromolecule #63: Large ribosomal subunit protein bL27m
+Macromolecule #64: Large ribosomal subunit protein bL28m
+Macromolecule #65: Large ribosomal subunit protein uL29m
+Macromolecule #66: Large ribosomal subunit protein uL30m
+Macromolecule #67: Small ribosomal subunit protein mS26
+Macromolecule #68: Large ribosomal subunit protein bL31m
+Macromolecule #69: Large ribosomal subunit protein bL32m
+Macromolecule #70: Large ribosomal subunit protein bL33m
+Macromolecule #71: Large ribosomal subunit protein bL34m
+Macromolecule #72: Large ribosomal subunit protein bL35m
+Macromolecule #73: Large ribosomal subunit protein mL58
+Macromolecule #74: Large ribosomal subunit protein mL59
+Macromolecule #75: Large ribosomal subunit protein mL60
+Macromolecule #76: Large ribosomal subunit protein mL67
+Macromolecule #35: E/E-site formyl-methionine tRNA
+Macromolecule #46: 21S mitochondrial rRNA
+Macromolecule #77: 15S mitochondrial rRNA
+Macromolecule #78: MAGNESIUM ION
+Macromolecule #79: GUANOSINE-5'-TRIPHOSPHATE
-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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| Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 200 |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Software | Name: EPU |
| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.0 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: 2.6 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
| Initial model |
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| Output model | ![]() PDB-9hm0: |
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Keywords
Authors
Sweden, 1 items
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Z (Sec.)
Y (Row.)
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FIELD EMISSION GUN


