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Yorodumi- EMDB-16966: Small subunit of yeast mitochondrial ribosome in complex with MET... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16966 | |||||||||
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Title | Small subunit of yeast mitochondrial ribosome in complex with METTL17/Rsm22. | |||||||||
Map data | Oversampled composite map of local-mask refined maps with sharpening and local resolution filtering | |||||||||
Sample |
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Keywords | mitochondria / assembly / biogenesis / iron-sulfur cluster / 4Fe-4S / RIBOSOME | |||||||||
Function / homology | Function and homology information Branched-chain amino acid catabolism / mitochondrial small ribosomal subunit assembly / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial translational initiation / valine catabolic process / Mitochondrial protein degradation / mitochondrial ribosome assembly / mitochondrial small ribosomal subunit / mitochondrial ribosome ...Branched-chain amino acid catabolism / mitochondrial small ribosomal subunit assembly / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial translational initiation / valine catabolic process / Mitochondrial protein degradation / mitochondrial ribosome assembly / mitochondrial small ribosomal subunit / mitochondrial ribosome / sporulation resulting in formation of a cellular spore / mitochondrial translation / superoxide dismutase activity / methyltransferase activity / mRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / peroxisome / ribosomal small subunit assembly / 4 iron, 4 sulfur cluster binding / small ribosomal subunit / mitochondrial inner membrane / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / GTP binding / mitochondrion / RNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.57 Å | |||||||||
Authors | Itoh Y / Chicherin I / Kamenski P / Amunts A | |||||||||
Funding support | European Union, Sweden, 2 items
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Citation | Journal: Mol Cell / Year: 2024 Title: METTL17 is an Fe-S cluster checkpoint for mitochondrial translation. Authors: Tslil Ast / Yuzuru Itoh / Shayan Sadre / Jason G McCoy / Gil Namkoong / Jordan C Wengrod / Ivan Chicherin / Pallavi R Joshi / Piotr Kamenski / Daniel L M Suess / Alexey Amunts / Vamsi K Mootha / Abstract: Friedreich's ataxia (FA) is a debilitating, multisystemic disease caused by the depletion of frataxin (FXN), a mitochondrial iron-sulfur (Fe-S) cluster biogenesis factor. To understand the cellular ...Friedreich's ataxia (FA) is a debilitating, multisystemic disease caused by the depletion of frataxin (FXN), a mitochondrial iron-sulfur (Fe-S) cluster biogenesis factor. To understand the cellular pathogenesis of FA, we performed quantitative proteomics in FXN-deficient human cells. Nearly every annotated Fe-S cluster-containing protein was depleted, indicating that as a rule, cluster binding confers stability to Fe-S proteins. We also observed depletion of a small mitoribosomal assembly factor METTL17 and evidence of impaired mitochondrial translation. Using comparative sequence analysis, mutagenesis, biochemistry, and cryoelectron microscopy, we show that METTL17 binds to the mitoribosomal small subunit during late assembly and harbors a previously unrecognized [FeS] cluster required for its stability. METTL17 overexpression rescued the mitochondrial translation and bioenergetic defects, but not the cellular growth, of FXN-depleted cells. These findings suggest that METTL17 acts as an Fe-S cluster checkpoint, promoting translation of Fe-S cluster-rich oxidative phosphorylation (OXPHOS) proteins only when Fe-S cofactors are replete. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16966.map.gz | 1 GB | EMDB map data format | |
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Header (meta data) | emd-16966-v30.xml emd-16966.xml | 58.5 KB 58.5 KB | Display Display | EMDB header |
Images | emd_16966.png | 132.2 KB | ||
Filedesc metadata | emd-16966.cif.gz | 14.5 KB | ||
Others | emd_16966_additional_1.map.gz | 379.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16966 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16966 | HTTPS FTP |
-Validation report
Summary document | emd_16966_validation.pdf.gz | 446.3 KB | Display | EMDB validaton report |
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Full document | emd_16966_full_validation.pdf.gz | 445.9 KB | Display | |
Data in XML | emd_16966_validation.xml.gz | 9 KB | Display | |
Data in CIF | emd_16966_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16966 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16966 | HTTPS FTP |
-Related structure data
Related structure data | 8om2MC 8om3C 8om4C C: citing same article (ref.) M: atomic model generated by this map |
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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_16966.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Oversampled composite map of local-mask refined maps with sharpening and local resolution filtering | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.59286 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Composite map of local-mask refined maps without sharpening
File | emd_16966_additional_1.map | ||||||||||||
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Annotation | Composite map of local-mask refined maps without sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Small subunit of mitochondrial ribosome in complex with METTL17/Rsm22
+Supramolecule #1: Small subunit of mitochondrial ribosome in complex with METTL17/Rsm22
+Macromolecule #1: 37S ribosomal protein MRP51, mitochondrial
+Macromolecule #2: 37S ribosomal protein MRP4, mitochondrial
+Macromolecule #3: Ribosomal protein VAR1, mitochondrial
+Macromolecule #4: 37S ribosomal protein NAM9, mitochondrial
+Macromolecule #5: 37S ribosomal protein S5, mitochondrial
+Macromolecule #6: 37S ribosomal protein MRP17, mitochondrial
+Macromolecule #7: 37S ribosomal protein S7, mitochondrial
+Macromolecule #8: 37S ribosomal protein S8, mitochondrial
+Macromolecule #9: 37S ribosomal protein S9, mitochondrial
+Macromolecule #10: 37S ribosomal protein S10, mitochondrial
+Macromolecule #11: 37S ribosomal protein S18, mitochondrial
+Macromolecule #12: 37S ribosomal protein S12, mitochondrial
+Macromolecule #13: 37S ribosomal protein SWS2, mitochondrial
+Macromolecule #14: 37S ribosomal protein MRP2, mitochondrial
+Macromolecule #15: 37S ribosomal protein S28, mitochondrial
+Macromolecule #16: 37S ribosomal protein S16, mitochondrial
+Macromolecule #17: 37S ribosomal protein S17, mitochondrial
+Macromolecule #18: 37S ribosomal protein RSM18, mitochondrial
+Macromolecule #19: 37S ribosomal protein S19, mitochondrial
+Macromolecule #20: 37S ribosomal protein MRP21, mitochondrial
+Macromolecule #21: 37S ribosomal protein S25, mitochondrial
+Macromolecule #22: 37S ribosomal protein PET123, mitochondrial
+Macromolecule #23: 37S ribosomal protein S23, mitochondrial
+Macromolecule #24: Mitochondrial 37S ribosomal protein S27
+Macromolecule #25: 37S ribosomal protein S24, mitochondrial
+Macromolecule #26: 37S ribosomal protein MRP10, mitochondrial
+Macromolecule #27: Mitochondrial mRNA-processing protein COX24
+Macromolecule #28: Protein FYV4, mitochondrial
+Macromolecule #29: 37S ribosomal protein S26, mitochondrial
+Macromolecule #30: 37S ribosomal protein MRP1, mitochondrial
+Macromolecule #31: 37S ribosomal protein MRP13, mitochondrial
+Macromolecule #32: 37S ribosomal protein S35, mitochondrial
+Macromolecule #33: 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
+Macromolecule #35: Probable S-adenosyl-L-methionine-dependent RNA methyltransferase ...
+Macromolecule #34: 15S mitochondrial rRNA
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: POTASSIUM ION
+Macromolecule #38: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #39: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #40: IRON/SULFUR CLUSTER
+Macromolecule #41: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 40 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 283744 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |