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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 | |||||||||
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Keywords | mitochondria / maturation / biogenesis / ribosome / GTPBP7 / GTPBP10 / GTP Binding Protein 10 / OBGH2 / MTG1 / LSU | |||||||||
| Function / homology | Function and homology informationmRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / mitochondrial RNA modification / regulation of respiratory system process / mitochondrial RNA catabolic process / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis ...mRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / mitochondrial RNA modification / regulation of respiratory system process / mitochondrial RNA catabolic process / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / protein lipoylation / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / positive regulation of mitochondrial translation / rRNA import into mitochondrion / RNA methyltransferase activity / Respiratory electron transport / rRNA methyltransferase activity / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / translation release factor activity / camera-type eye development / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit / mitochondrial fission / peptidyl-tRNA hydrolase / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / mitochondrial ribosome / mitochondrial small ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase activity / rRNA methylation / mitochondrial translation / [2Fe-2S] cluster assembly / protein targeting to mitochondrion / iron-sulfur cluster assembly / acyl binding / ribosomal large subunit binding / acyl carrier activity / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / anatomical structure morphogenesis / RNA processing / rescue of stalled cytosolic ribosome / Mitochondrial protein degradation / aerobic respiration / Transferases; Transferring one-carbon groups; Methyltransferases / fatty acid binding / cellular response to leukemia inhibitory factor / ribosomal large subunit biogenesis / methyltransferase activity / mitochondrial membrane / fibrillar center / rRNA processing / fatty acid biosynthetic process / cell junction / double-stranded RNA binding / ribosome biogenesis / chromosome / heart development / 5S rRNA binding / small ribosomal subunit rRNA binding / double-stranded DNA binding / large ribosomal subunit rRNA binding / endonuclease activity / negative regulation of translation / mitochondrial inner membrane / 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 / calcium ion binding / regulation of DNA-templated transcription / GTP binding / nucleolus / structural molecule activity / magnesium ion binding / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus 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 |
-Validation report
| Summary document | emd_17719_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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| Full document | emd_17719_full_validation.pdf.gz | 1.2 MB | Display | |
| Data in XML | emd_17719_validation.xml.gz | 18.1 KB | Display | |
| Data in CIF | emd_17719_validation.cif.gz | 21.7 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17719 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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

