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- EMDB-27249: Yeast mitochondrial small subunit assembly intermediate (State 1) -
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Open data
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Basic information
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Title | Yeast mitochondrial small subunit assembly intermediate (State 1) | |||||||||
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![]() | Ribonucleoprotein complex Mitochondria Biogenesis / RIBOSOME | |||||||||
Function / homology | ![]() 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 / small ribosomal subunit rRNA binding / methylation ...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 / small ribosomal subunit rRNA binding / methylation / cytosolic small ribosomal subunit / mitochondrial inner membrane / rRNA binding / structural constituent of ribosome / translation / mitochondrion / RNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Burnside C / Harper N / Klinge S | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 227.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 35.4 KB 35.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 46.9 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 9.9 KB | ||
Others | ![]() ![]() | 193.3 MB 192.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Full map | ||||||||||||||||||||
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
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Density Histograms |
-Half map: #1
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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 | ||||||||||||
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Density Histograms |
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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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: ![]() |
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 |