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Yorodumi- EMDB-26966: Human mitochondrial small subunit assembly intermediate (State A) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26966 | |||||||||
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Title | Human mitochondrial small subunit assembly intermediate (State A) | |||||||||
Map data | Mitochondrial small subunit assembly intermediate (State A) | |||||||||
Sample |
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Keywords | Ribonucleoprotein complex / Mitochondria Biogenesis / RIBOSOME | |||||||||
Function / homology | Function and homology information : / mitochondrial small ribosomal subunit assembly / rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / Mitochondrial Fatty Acid Beta-Oxidation / mitochondrial ribosome binding / [acyl-carrier-protein] S-malonyltransferase ...: / mitochondrial small ribosomal subunit assembly / rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / Mitochondrial Fatty Acid Beta-Oxidation / mitochondrial ribosome binding / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / S-adenosyl-L-methionine binding / regulation of cellular respiration / mitochondrial small ribosomal subunit / rRNA methylation / mitochondrial ribosome / fatty acid beta-oxidation / mitochondrial translation / mitochondrial nucleoid / ribosomal small subunit binding / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / apoptotic signaling pathway / Transcriptional activation of mitochondrial biogenesis / fatty acid biosynthetic process / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / 4 iron, 4 sulfur cluster binding / small ribosomal subunit / nuclear membrane / cell population proliferation / tRNA binding / mitochondrial inner membrane / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / protein domain specific binding / mRNA binding / GTP binding / nucleolus / apoptotic process / mitochondrion / DNA binding / RNA binding / nucleoplasm / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.66 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_26966.map.gz | 228.4 MB | EMDB map data format | |
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Header (meta data) | emd-26966-v30.xml emd-26966.xml | 56.5 KB 56.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26966_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_26966.png | 72.3 KB | ||
Masks | emd_26966_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-26966.cif.gz | 13.9 KB | ||
Others | emd_26966_half_map_1.map.gz emd_26966_half_map_2.map.gz | 192.4 MB 192.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26966 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26966 | HTTPS FTP |
-Validation report
Summary document | emd_26966_validation.pdf.gz | 973.6 KB | Display | EMDB validaton report |
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Full document | emd_26966_full_validation.pdf.gz | 973.2 KB | Display | |
Data in XML | emd_26966_validation.xml.gz | 22 KB | Display | |
Data in CIF | emd_26966_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26966 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26966 | HTTPS FTP |
-Related structure data
Related structure data | 8cspMC 8csqC 8csrC 8cssC 8cstC 8csuC 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_26966.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Mitochondrial small subunit assembly intermediate (State A) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_26966_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Mitochondrial small subunit assembly intermediate (State A)
File | emd_26966_half_map_1.map | ||||||||||||
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Annotation | Mitochondrial small subunit assembly intermediate (State A) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Mitochondrial small subunit assembly intermediate (State A)
File | emd_26966_half_map_2.map | ||||||||||||
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Annotation | Mitochondrial small subunit assembly intermediate (State A) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human mitochondrial small subunit assembly intermediate, State A
+Supramolecule #1: Human mitochondrial small subunit assembly intermediate, State A
+Macromolecule #1: 28S ribosomal protein S34, mitochondrial
+Macromolecule #2: 28S ribosomal protein S35, mitochondrial
+Macromolecule #3: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #4: Dimethyladenosine transferase 1, mitochondrial
+Macromolecule #5: Methyltransferase-like protein 17, mitochondrial
+Macromolecule #6: Malonyl-CoA-acyl carrier protein transacylase, mitochondrial
+Macromolecule #7: Nitric oxide-associated protein 1
+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 S12, mitochondrial
+Macromolecule #17: 28S ribosomal protein S14, mitochondrial
+Macromolecule #18: 28S ribosomal protein S15, mitochondrial
+Macromolecule #19: 28S ribosomal protein S16, mitochondrial
+Macromolecule #20: 28S ribosomal protein S17, mitochondrial
+Macromolecule #21: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #22: 28S ribosomal protein S18c, mitochondrial
+Macromolecule #23: 28S ribosomal protein S21, mitochondrial
+Macromolecule #24: 28S ribosomal protein S22, mitochondrial
+Macromolecule #25: 28S ribosomal protein S23, mitochondrial
+Macromolecule #26: 28S ribosomal protein S25, mitochondrial
+Macromolecule #27: 28S ribosomal protein S26, mitochondrial
+Macromolecule #28: 28S ribosomal protein S27, mitochondrial
+Macromolecule #29: 28S ribosomal protein S28, mitochondrial
+Macromolecule #30: 28S ribosomal protein S29, mitochondrial
+Macromolecule #31: 28S ribosomal protein S31, mitochondrial
+Macromolecule #32: 28S ribosomal protein S33, mitochondrial
+Macromolecule #33: GTPase Era, 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: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #39: ZINC ION
+Macromolecule #40: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #41: 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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Grid | Model: Quantifoil R3.5/1 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
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: 47037 / Average electron dose: 51.0 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: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL | ||||||||
Output model | PDB-8csp: |