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Yorodumi- EMDB-17719: human mitoribosomal large subunit assembly intermediate 1 with GT... -
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Open data
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Basic information
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| Title | human mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7 | |||||||||
Map data | full map, sharpened | |||||||||
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Keywords | mitochondria / maturation / biogenesis / ribosome / GTPBP7 / GTPBP10 / GTP Binding Protein 10 / OBGH2 / MTG1 / LSU | |||||||||
| Function / homology | Function and homology informationmitochondrial ribosomal large subunit rRNA binding / regulation of respiratory system process / rRNA modification in the mitochondrion / mitochondrial RNA modification / mRNA (cytidine-5-)-methyltransferase activity / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial RNA catabolic process / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis ...mitochondrial ribosomal large subunit rRNA binding / regulation of respiratory system process / rRNA modification in the mitochondrion / mitochondrial RNA modification / mRNA (cytidine-5-)-methyltransferase activity / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial RNA catabolic process / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / protein-RNA adaptor activity / Protein lipoylation / Complex I biogenesis / positive regulation of mitochondrial translation / RNA methyltransferase activity / Respiratory electron transport / mitochondrial large ribosomal subunit assembly / rRNA methyltransferase activity / rRNA import into mitochondrion / rescue of stalled mitochondrial ribosome / mitochondrial translational termination / RNA folding chaperone / mitochondrial translational elongation / iron-sulfur cluster assembly complex / translation release factor activity, codon nonspecific / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation initiation / protein lipoylation / mitochondrial fission / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / rRNA methylation / mitochondrial ribosome / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / [2Fe-2S] cluster assembly / mitochondrial translation / iron-sulfur cluster assembly / ribosomal large subunit binding / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / acyl binding / mitochondrial respiratory chain complex I assembly / respiratory chain complex I / anatomical structure morphogenesis / acyl carrier activity / RNA processing / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / aerobic respiration / fatty acid binding / methyltransferase activity / ribosomal large subunit biogenesis / mitochondrial membrane / fatty acid biosynthetic process / rRNA processing / regulation of translation / double-stranded RNA binding / chromosome / 5S rRNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / mitochondrial inner membrane / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / GTPase activity / calcium ion binding / apoptotic process / nucleolus / GTP binding / structural molecule activity / magnesium ion binding / mitochondrion / : / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.03 Å | |||||||||
Authors | Kummer E / Nguyen TG / Ritter C | |||||||||
| Funding support | Denmark, 1 items
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Citation | Journal: Nat Commun / Year: 2023Title: Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome. Authors: Thu Giang Nguyen / Christina Ritter / Eva Kummer / ![]() Abstract: Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ...Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ribosomal proteins. Assembly is coordinated in the mitochondrial matrix by biogenesis factors that transiently associate with the maturing particle. Here, we present a structural snapshot of a large mitoribosomal subunit assembly intermediate containing 7 biogenesis factors including the GTPases GTPBP7 and GTPBP10. Our structure illustrates how GTPBP10 aids the folding of the ribosomal RNA during the biogenesis process, how this process is related to bacterial ribosome biogenesis, and why mitochondria require two biogenesis factors in contrast to only one in bacteria. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_17719.map.gz | 398.3 MB | EMDB map data format | |
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| Header (meta data) | emd-17719-v30.xml emd-17719.xml | 87.4 KB 87.4 KB | Display Display | EMDB header |
| Images | emd_17719.png | 96.9 KB | ||
| Masks | emd_17719_msk_1.map | 421.9 MB | Mask map | |
| Filedesc metadata | emd-17719.cif.gz | 18.4 KB | ||
| Others | emd_17719_additional_1.map.gz emd_17719_half_map_1.map.gz emd_17719_half_map_2.map.gz | 212.1 MB 391.2 MB 391.3 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17719 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17719 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8pk0MC ![]() 8qsjC 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_17719.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | full map, sharpened | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_17719_msk_1.map | ||||||||||||
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-Additional map: full map, unsharpened
| File | emd_17719_additional_1.map | ||||||||||||
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| Annotation | full map, unsharpened | ||||||||||||
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-Half map: #2
| File | emd_17719_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_17719_half_map_2.map | ||||||||||||
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Sample components
+Entire : large mitoribosomal subunit biogenesis intermediate with GTPBP10,...
+Supramolecule #1: large mitoribosomal subunit biogenesis intermediate with GTPBP10,...
+Macromolecule #1: 39S ribosomal protein L32, mitochondrial
+Macromolecule #2: 39S ribosomal protein L22, mitochondrial
+Macromolecule #3: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #4: 39S ribosomal protein L33, mitochondrial
+Macromolecule #5: 39S ribosomal protein L23, mitochondrial
+Macromolecule #6: MIEF1 upstream open reading frame protein
+Macromolecule #7: 39S ribosomal protein L34, mitochondrial
+Macromolecule #8: 39S ribosomal protein L24, mitochondrial
+Macromolecule #9: Acyl carrier protein, mitochondrial
+Macromolecule #10: 39S ribosomal protein L35, mitochondrial
+Macromolecule #11: 39S ribosomal protein L27, mitochondrial
+Macromolecule #12: 5-methylcytosine rRNA methyltransferase NSUN4
+Macromolecule #13: 39S ribosomal protein L37, mitochondrial
+Macromolecule #14: 39S ribosomal protein L28, mitochondrial
+Macromolecule #15: Transcription termination factor 4, mitochondrial
+Macromolecule #16: 39S ribosomal protein L38, mitochondrial
+Macromolecule #17: 39S ribosomal protein L47, mitochondrial
+Macromolecule #18: Mitochondrial ribosome-associated GTPase 1
+Macromolecule #19: 39S ribosomal protein L39, mitochondrial
+Macromolecule #20: 39S ribosomal protein L30, mitochondrial
+Macromolecule #21: 39S ribosomal protein L40, mitochondrial
+Macromolecule #22: 39S ribosomal protein L42, mitochondrial
+Macromolecule #23: 39S ribosomal protein L41, mitochondrial
+Macromolecule #24: Large ribosomal subunit protein mL43
+Macromolecule #26: 39S ribosomal protein L44, mitochondrial
+Macromolecule #28: 39S ribosomal protein L45, mitochondrial
+Macromolecule #29: 39S ribosomal protein L2, mitochondrial
+Macromolecule #30: 39S ribosomal protein L46, mitochondrial
+Macromolecule #31: 39S ribosomal protein L3, mitochondrial
+Macromolecule #32: 39S ribosomal protein L48, mitochondrial
+Macromolecule #33: 39S ribosomal protein L4, mitochondrial
+Macromolecule #34: 39S ribosomal protein L49, mitochondrial
+Macromolecule #35: 39S ribosomal protein L9, mitochondrial
+Macromolecule #36: 39S ribosomal protein L50, mitochondrial
+Macromolecule #37: 39S ribosomal protein L10, mitochondrial
+Macromolecule #38: 39S ribosomal protein L51, mitochondrial
+Macromolecule #39: 39S ribosomal protein L11, mitochondrial
+Macromolecule #40: 39S ribosomal protein L52, mitochondrial
+Macromolecule #41: 39S ribosomal protein L13, mitochondrial
+Macromolecule #42: 39S ribosomal protein L53, mitochondrial
+Macromolecule #43: 39S ribosomal protein L14, mitochondrial
+Macromolecule #44: 39S ribosomal protein L54, mitochondrial
+Macromolecule #45: 39S ribosomal protein L15, mitochondrial
+Macromolecule #46: 39S ribosomal protein L55, mitochondrial
+Macromolecule #47: 39S ribosomal protein L16, mitochondrial
+Macromolecule #48: Ribosomal protein 63, mitochondrial
+Macromolecule #49: 39S ribosomal protein L17, mitochondrial
+Macromolecule #50: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #51: 39S ribosomal protein L18, mitochondrial
+Macromolecule #52: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #53: 39S ribosomal protein L19, mitochondrial
+Macromolecule #54: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #55: 39S ribosomal protein L20, mitochondrial
+Macromolecule #56: 39S ribosomal protein S30, mitochondrial
+Macromolecule #57: 39S ribosomal protein L21, mitochondrial
+Macromolecule #58: GTP-binding protein 10
+Macromolecule #25: 16S rRNA + pre-H68-71 segment
+Macromolecule #27: CP tRNA-Val
+Macromolecule #59: ZINC ION
+Macromolecule #60: S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYL...
+Macromolecule #61: S-ADENOSYLMETHIONINE
+Macromolecule #62: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #63: MAGNESIUM ION
+Macromolecule #64: POTASSIUM ION
-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: 7.6 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / 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: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
Denmark, 1 items
Citation




















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Processing
FIELD EMISSION GUN

