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Yorodumi- EMDB-47791: Mouse mitoribosome large subunit assembly intermediate bound to N... -
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Basic information
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| Title | Mouse mitoribosome large subunit assembly intermediate bound to NSUN4, METRF4, GTPBP7, GTPBP10 and the MALSU1-L0R8F8-mt-ACP complex (without uL16m), State B1 (SAMC knock-out) | ||||||||||||
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Keywords | mitochondria / ribosome assembly / large subunit / ribosome | ||||||||||||
| Function / homology | Function and homology informationMitochondrial ribosome-associated quality control / Mitochondrial translation elongation / mitochondrial small ribosomal subunit assembly / mRNA (cytidine-5-)-methyltransferase activity / regulation of respiratory system process / regulation of mitochondrial transcription / Mitochondrial translation termination / mitochondrial RNA catabolic process / regulation of mitochondrial translation / negative regulation of mitochondrial translation ...Mitochondrial ribosome-associated quality control / Mitochondrial translation elongation / mitochondrial small ribosomal subunit assembly / mRNA (cytidine-5-)-methyltransferase activity / regulation of respiratory system process / regulation of mitochondrial transcription / Mitochondrial translation termination / mitochondrial RNA catabolic process / regulation of mitochondrial translation / negative regulation of mitochondrial translation / rRNA (cytosine-C5-)-methyltransferase activity / mitochondrial large ribosomal subunit assembly / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / negative regulation of ribosome biogenesis / Complex I biogenesis / positive regulation of mitochondrial translation / Respiratory electron transport / rRNA import into mitochondrion / ribonuclease III activity / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / Mitochondrial protein degradation / translation release factor activity, codon nonspecific / camera-type eye development / mitochondrial fission / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / translation release factor activity / mitochondrial [2Fe-2S] assembly complex / mitochondrial ribosome / rRNA methylation / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / [2Fe-2S] cluster assembly / mitochondrial translation / iron-sulfur cluster assembly / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I assembly / respiratory chain complex I / RNA processing / rescue of stalled cytosolic ribosome / cytosolic ribosome / Transferases; Transferring one-carbon groups; Methyltransferases / aerobic respiration / cellular response to leukemia inhibitory factor / ribosomal large subunit biogenesis / mitochondrion organization / fibrillar center / fatty acid biosynthetic process / rRNA processing / cell junction / double-stranded RNA binding / large ribosomal subunit / ribosome biogenesis / heart development / 5S rRNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / mitochondrial inner membrane / negative regulation of translation / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / GTPase activity / mRNA binding / apoptotic process / GTP binding / nucleolus / structural molecule activity / magnesium ion binding / mitochondrion / RNA binding / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||
| Biological species | ![]() | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.62 Å | ||||||||||||
Authors | Singh V / Glasgow RIC / Rorbach J / Freyer C / Amunts A / Wredenberg A | ||||||||||||
| Funding support | Sweden, Denmark, 3 items
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Citation | Journal: Nat Commun / Year: 2025Title: The mitochondrial methylation potential gates mitoribosome assembly. Authors: Ruth I C Glasgow / Vivek Singh / Lucía Peña-Pérez / Alissa Wilhalm / Marco F Moedas / David Moore / Florian A Rosenberger / Xinping Li / Ilian Atanassov / Mira Saba / Miriam Cipullo / ...Authors: Ruth I C Glasgow / Vivek Singh / Lucía Peña-Pérez / Alissa Wilhalm / Marco F Moedas / David Moore / Florian A Rosenberger / Xinping Li / Ilian Atanassov / Mira Saba / Miriam Cipullo / Joanna Rorbach / Anna Wedell / Christoph Freyer / Alexey Amunts / Anna Wredenberg / ![]() Abstract: S-adenosylmethionine (SAM) is the principal methyl donor in cells and is essential for mitochondrial gene expression, influencing RNA modifications, translation, and ribosome biogenesis. Using direct ...S-adenosylmethionine (SAM) is the principal methyl donor in cells and is essential for mitochondrial gene expression, influencing RNA modifications, translation, and ribosome biogenesis. Using direct long-read RNA sequencing in mouse tissues and embryonic fibroblasts, we show that processing of the mitochondrial ribosomal gene cluster fails in the absence of mitochondrial SAM, leading to an accumulation of unprocessed precursors. Proteomic analysis of ribosome fractions revealed these precursors associated with processing and assembly factors, indicating stalled biogenesis. Structural analysis by cryo-electron microscopy demonstrated that SAM-dependent methylation is required for peptidyl transferase centre formation during mitoribosome assembly. Our findings identify a critical role for SAM in coordinating mitoribosomal RNA processing and large subunit maturation, linking cellular methylation potential to mitochondrial translation capacity. | ||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_47791.map.gz | 487.5 MB | EMDB map data format | |
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| Header (meta data) | emd-47791-v30.xml emd-47791.xml | 80.4 KB 80.4 KB | Display Display | EMDB header |
| Images | emd_47791.png | 71.3 KB | ||
| Filedesc metadata | emd-47791.cif.gz | 17 KB | ||
| Others | emd_47791_additional_1.map.gz emd_47791_half_map_1.map.gz emd_47791_half_map_2.map.gz | 282.8 MB 488.5 MB 488.5 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-47791 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-47791 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9e9cMC ![]() 9hccC ![]() 9hcdC ![]() 9hceC ![]() 9hcfC ![]() 9hcgC ![]() 9hchC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_47791.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.84684 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: #1
| File | emd_47791_additional_1.map | ||||||||||||
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-Half map: #2
| File | emd_47791_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_47791_half_map_2.map | ||||||||||||
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Sample components
+Entire : mitoribosome large subunit assembly intermediate
+Supramolecule #1: mitoribosome large subunit assembly intermediate
+Macromolecule #1: RNA (1428-MER)
+Macromolecule #2: RNA (56-MER)
+Macromolecule #3: Large ribosomal subunit protein uL2m
+Macromolecule #4: Large ribosomal subunit protein uL3m
+Macromolecule #5: Large ribosomal subunit protein uL4m
+Macromolecule #6: Large ribosomal subunit protein bL9m
+Macromolecule #7: Large ribosomal subunit protein uL10m
+Macromolecule #8: Large ribosomal subunit protein uL11m
+Macromolecule #9: Large ribosomal subunit protein uL13m
+Macromolecule #10: Large ribosomal subunit protein uL14m
+Macromolecule #11: Large ribosomal subunit protein uL15m
+Macromolecule #12: Large ribosomal subunit protein bL17m
+Macromolecule #13: Large ribosomal subunit protein uL18m
+Macromolecule #14: Large ribosomal subunit protein bL19m
+Macromolecule #15: Large ribosomal subunit protein bL20m
+Macromolecule #16: Large ribosomal subunit protein bL21m
+Macromolecule #17: Large ribosomal subunit protein uL22m
+Macromolecule #18: Large ribosomal subunit protein uL23m
+Macromolecule #19: Large ribosomal subunit protein uL24m
+Macromolecule #20: Large ribosomal subunit protein bL27m
+Macromolecule #21: Large ribosomal subunit protein bL28m
+Macromolecule #22: Large ribosomal subunit protein uL29m
+Macromolecule #23: Large ribosomal subunit protein uL30m
+Macromolecule #24: 5-cytosine rRNA methyltransferase NSUN4
+Macromolecule #25: Large ribosomal subunit protein bL32m
+Macromolecule #26: Large ribosomal subunit protein bL33m
+Macromolecule #27: Large ribosomal subunit protein bL34m
+Macromolecule #28: Large ribosomal subunit protein bL35m
+Macromolecule #29: Large ribosomal subunit protein bL36m
+Macromolecule #30: Large ribosomal subunit protein mL38
+Macromolecule #31: Large ribosomal subunit protein mL39
+Macromolecule #32: Large ribosomal subunit protein mL43
+Macromolecule #33: Large ribosomal subunit protein mL44
+Macromolecule #34: Large ribosomal subunit protein mL45
+Macromolecule #35: Large ribosomal subunit protein mL46
+Macromolecule #36: Large ribosomal subunit protein mL48
+Macromolecule #37: Large ribosomal subunit protein mL49
+Macromolecule #38: Large ribosomal subunit protein mL50
+Macromolecule #39: Large ribosomal subunit protein mL51
+Macromolecule #40: Large ribosomal subunit protein mL52
+Macromolecule #41: Large ribosomal subunit protein mL53
+Macromolecule #42: Large ribosomal subunit protein mL63
+Macromolecule #43: Large ribosomal subunit protein mL62
+Macromolecule #44: Large ribosomal subunit protein mL64
+Macromolecule #45: Large ribosomal subunit protein mL66
+Macromolecule #46: Large ribosomal subunit protein mL65
+Macromolecule #47: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #48: Predicted gene, 55359
+Macromolecule #49: Acyl carrier protein, mitochondrial
+Macromolecule #50: Large ribosomal subunit protein mL37
+Macromolecule #51: Large ribosomal subunit protein mL40
+Macromolecule #52: Large ribosomal subunit protein mL41
+Macromolecule #53: Large ribosomal subunit protein mL42
+Macromolecule #54: Large ribosomal subunit protein mL55
+Macromolecule #55: Mitochondrial ribosome-associated GTPase 1
+Macromolecule #56: Large ribosomal subunit protein mL54
+Macromolecule #57: Transcription termination factor 4, mitochondrial
+Macromolecule #58: GTP-binding protein 10
+Macromolecule #59: MAGNESIUM ION
+Macromolecule #60: ZINC ION
+Macromolecule #61: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #62: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 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: 2.0 µm / Nominal defocus min: 0.4 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Authors
Sweden,
Denmark, 3 items
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Processing
FIELD EMISSION GUN

