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Yorodumi- EMDB-17719: human mitoribosomal large subunit assembly intermediate 1 with GT... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17719 | |||||||||
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Title | human mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7 | |||||||||
Map data | full map, sharpened | |||||||||
Sample |
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Keywords | mitochondria / maturation / biogenesis / ribosome / GTPBP7 / GTPBP10 / GTP Binding Protein 10 / OBGH2 / MTG1 / LSU | |||||||||
Function / homology | Function and homology information regulation of respiratory system process / tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis ...regulation of respiratory system process / tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport / rRNA methyltransferase activity / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / protein targeting to mitochondrion / camera-type eye development / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit / mitochondrial fission / mitochondrial large ribosomal subunit binding / peptidyl-tRNA hydrolase / mitochondrial ribosome / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial small ribosomal subunit / rRNA methylation / mitochondrial translation / aminoacyl-tRNA hydrolase activity / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / : / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / acyl binding / anatomical structure morphogenesis / acyl carrier activity / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / ribosomal large subunit biogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to leukemia inhibitory factor / methyltransferase activity / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / rRNA processing / double-stranded RNA binding / small ribosomal subunit rRNA binding / cell junction / ribosome biogenesis / heart development / chromosome / large ribosomal subunit rRNA binding / 5S rRNA binding / double-stranded DNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / GTPase activity / mRNA binding / nucleotide binding / calcium ion binding / synapse / regulation of DNA-templated transcription / nucleolus / GTP binding / apoptotic process / magnesium ion binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / 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: 2023 Title: 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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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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 | 79.6 KB 79.6 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 | 17 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 | 21.5 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 (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_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 | ||||||||||||||||||||||||||||||||||||
Density |
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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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Projections & Slices |
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Density Histograms |
-Additional map: full map, unsharpened
File | emd_17719_additional_1.map | ||||||||||||
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Annotation | full map, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17719_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17719_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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 |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31656 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |