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Yorodumi- EMDB-26971: Human mitochondrial small subunit assembly intermediate (State C*) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26971 | |||||||||
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Title | Human mitochondrial small subunit assembly intermediate (State C*)Mitochondrion | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA modification / mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination ...rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA modification / mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / S-adenosyl-L-methionine binding / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit / rRNA methylation / mitochondrial ribosome / mitochondrial translation / mitochondrial nucleoid / positive regulation of proteolysis / ribosomal small subunit binding / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / apoptotic signaling pathway / Transcriptional activation of mitochondrial biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / regulation of translation / cell junction / small ribosomal subunit / methylation / nuclear membrane / mitochondrial inner membrane / cell population proliferation / tRNA binding / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / translation / protein domain specific binding / mRNA binding / intracellular membrane-bounded organelle / GTP binding / nucleolus / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.03 Å | |||||||||
Authors | Harper NJ / Burnside C / 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_26971.map.gz | 228.6 MB | EMDB map data format | |
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Header (meta data) | emd-26971-v30.xml emd-26971.xml | 51.9 KB 51.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26971_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_26971.png | 67 KB | ||
Masks | emd_26971_msk_1.map | 244.1 MB | Mask map | |
Others | emd_26971_half_map_1.map.gz emd_26971_half_map_2.map.gz | 190.5 MB 189.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26971 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26971 | HTTPS FTP |
-Related structure data
Related structure data | 8csuMC 8cspC 8csqC 8csrC 8cssC 8cstC 8d8jC 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_26971.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.062 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26971_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26971_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26971_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human mitochondrial small subunit assembly intermediate, State C*
+Supramolecule #1: Human mitochondrial small subunit assembly intermediate, State C*
+Macromolecule #1: 28S ribosomal protein S34, mitochondrial
+Macromolecule #2: 28S ribosomal protein S35, mitochondrial
+Macromolecule #3: Aurora kinase A-interacting protein
+Macromolecule #4: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #5: Dimethyladenosine transferase 1, mitochondrial
+Macromolecule #6: Putative ribosome-binding factor A, mitochondrial
+Macromolecule #7: Methyltransferase-like protein 17, mitochondrial
+Macromolecule #9: 28S ribosomal protein S2, mitochondrial
+Macromolecule #10: 28S ribosomal protein S24, mitochondrial
+Macromolecule #11: 28S ribosomal protein S5, mitochondrial
+Macromolecule #12: 28S ribosomal protein S6, mitochondrial
+Macromolecule #13: 28S ribosomal protein S7, mitochondrial
+Macromolecule #14: 28S ribosomal protein S9, mitochondrial
+Macromolecule #15: 28S ribosomal protein S10, mitochondrial
+Macromolecule #16: 28S ribosomal protein S11, mitochondrial
+Macromolecule #17: 28S ribosomal protein S12, mitochondrial
+Macromolecule #18: 28S ribosomal protein S14, mitochondrial
+Macromolecule #19: 28S ribosomal protein S15, mitochondrial
+Macromolecule #20: 28S ribosomal protein S16, mitochondrial
+Macromolecule #21: 28S ribosomal protein S17, mitochondrial
+Macromolecule #22: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #23: 28S ribosomal protein S18c, mitochondrial
+Macromolecule #24: 28S ribosomal protein S21, mitochondrial
+Macromolecule #25: 28S ribosomal protein S22, mitochondrial
+Macromolecule #26: 28S ribosomal protein S23, mitochondrial
+Macromolecule #27: 28S ribosomal protein S25, mitochondrial
+Macromolecule #28: 28S ribosomal protein S26, mitochondrial
+Macromolecule #29: 28S ribosomal protein S27, mitochondrial
+Macromolecule #30: 28S ribosomal protein S28, mitochondrial
+Macromolecule #31: 28S ribosomal protein S29, mitochondrial
+Macromolecule #32: 28S ribosomal protein S31, mitochondrial
+Macromolecule #33: 28S ribosomal protein S33, mitochondrial
+Macromolecule #8: 12S mitochondrial rRNA
+Macromolecule #34: IRON/SULFUR CLUSTER
+Macromolecule #35: S-ADENOSYLMETHIONINE
+Macromolecule #36: POTASSIUM ION
+Macromolecule #37: MAGNESIUM ION
+Macromolecule #38: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #39: ZINC ION
+Macromolecule #40: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #41: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #42: GUANOSINE-5'-DIPHOSPHATE
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 47037 / Average electron dose: 51.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |