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Yorodumi- EMDB-27249: Yeast mitochondrial small subunit assembly intermediate (State 1) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27249 | |||||||||
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Title | Yeast mitochondrial small subunit assembly intermediate (State 1) | |||||||||
Map data | Full map | |||||||||
Sample |
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Keywords | Ribonucleoprotein complex Mitochondria Biogenesis / RIBOSOME | |||||||||
Function / homology | Function and homology information mitochondrial small ribosomal subunit assembly / mitochondrial small ribosomal subunit / sporulation resulting in formation of a cellular spore / mitochondrial translation / RNA splicing / methyltransferase activity / mRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / 4 iron, 4 sulfur cluster binding ...mitochondrial small ribosomal subunit assembly / mitochondrial small ribosomal subunit / sporulation resulting in formation of a cellular spore / mitochondrial translation / RNA splicing / methyltransferase activity / mRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / 4 iron, 4 sulfur cluster binding / small ribosomal subunit / mitochondrial inner membrane / rRNA binding / structural constituent of ribosome / translation / mitochondrion / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Burnside C / Harper N / Klinge S | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nature / Year: 2023 Title: Principles of mitoribosomal small subunit assembly in eukaryotes. Authors: Nathan J Harper / Chloe Burnside / Sebastian Klinge / Abstract: Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is ...Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is essential for ATP production and cellular metabolism. Here we used cryo-electron microscopy to determine nine structures of native yeast and human mitoribosomal small subunit assembly intermediates, illuminating the mechanistic basis for how GTPases are used to control early steps of decoding centre formation, how initial rRNA folding and processing events are mediated, and how mitoribosomal proteins have active roles during assembly. Furthermore, this series of intermediates from two species with divergent mitoribosomal architecture uncovers both conserved principles and species-specific adaptations that govern the maturation of mitoribosomal small subunits in eukaryotes. By revealing the dynamic interplay between assembly factors, mitoribosomal proteins and rRNA that are required to generate functional subunits, our structural analysis provides a vignette for how molecular complexity and diversity can evolve in large ribonucleoprotein assemblies. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27249.map.gz | 227.8 MB | EMDB map data format | |
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Header (meta data) | emd-27249-v30.xml emd-27249.xml | 35.4 KB 35.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27249_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_27249.png | 46.9 KB | ||
Masks | emd_27249_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-27249.cif.gz | 9.9 KB | ||
Others | emd_27249_half_map_1.map.gz emd_27249_half_map_2.map.gz | 193.3 MB 192.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27249 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27249 | HTTPS FTP |
-Validation report
Summary document | emd_27249_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_27249_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_27249_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | emd_27249_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27249 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27249 | HTTPS FTP |
-Related structure data
Related structure data | 8d8jMC 8cspC 8csqC 8csrC 8cssC 8cstC 8csuC 8d8kC 8d8lC 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_27249.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Full map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.057 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27249_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27249_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_27249_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Yeast mitochondrial small subunit assembly intermediate (State 3)
+Supramolecule #1: Yeast mitochondrial small subunit assembly intermediate (State 3)
+Macromolecule #1: Probable S-adenosyl-L-methionine-dependent RNA methyltransferase ...
+Macromolecule #2: 37S ribosomal protein MRP13, mitochondrial
+Macromolecule #3: Mitochondrial group I intron splicing factor CCM1
+Macromolecule #4: 37S ribosomal protein S28, mitochondrial
+Macromolecule #5: 37S ribosomal protein S16, mitochondrial
+Macromolecule #6: 37S ribosomal protein S17, mitochondrial
+Macromolecule #7: 37S ribosomal protein RSM18, mitochondrial
+Macromolecule #8: 37S ribosomal protein PET123, mitochondrial
+Macromolecule #9: Protein FYV4, mitochondrial
+Macromolecule #10: 37S ribosomal protein NAM9, mitochondrial
+Macromolecule #11: 37S ribosomal protein S5, mitochondrial
+Macromolecule #12: 37S ribosomal protein MRP17, mitochondrial
+Macromolecule #13: 37S ribosomal protein S35, mitochondrial
+Macromolecule #14: 37S ribosomal protein S8, mitochondrial
+Macromolecule #16: uS12m
+Macromolecule #15: 15S ribosomal RNA
+Macromolecule #17: IRON/SULFUR CLUSTER
+Macromolecule #18: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 14111 / Average electron dose: 61.73 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |