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Yorodumi- EMDB-17720: human mitoribosomal large subunit assembly intermediate 2 with GTPBP7 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17720 | |||||||||
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Title | human mitoribosomal large subunit assembly intermediate 2 with GTPBP7 | |||||||||
Map data | full map, sharpened | |||||||||
Sample |
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Keywords | mitochondria / maturation / biogenesis / ribosome / GTPBP7 / MTG1 / LSU | |||||||||
Function / homology | Function and homology information regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / tRNA (cytidine-5-)-methyltransferase activity / 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 / rRNA modification in the mitochondrion / regulation of mitochondrial translation / tRNA (cytidine-5-)-methyltransferase activity / 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 / rRNA methyltransferase activity / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / positive regulation of mitochondrial translation / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / iron-sulfur cluster assembly complex / protein targeting to mitochondrion / mitochondrial large ribosomal subunit binding / mitochondrial fission / camera-type eye development / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / rRNA methylation / [2Fe-2S] cluster assembly / aminoacyl-tRNA hydrolase activity / respiratory chain complex I / mitochondrial ribosome / iron-sulfur cluster assembly / mitochondrial translation / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / 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 / heart development / large ribosomal subunit rRNA binding / double-stranded DNA binding / 5S rRNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / GTPase activity / mRNA binding / nucleotide binding / calcium ion binding / synapse / GTP binding / regulation of DNA-templated transcription / nucleolus / apoptotic process / 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: 3.0 Å | |||||||||
Authors | Kummer E / Nguyen TG | |||||||||
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_17720.map.gz | 398.5 MB | EMDB map data format | |
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Header (meta data) | emd-17720-v30.xml emd-17720.xml | 21.7 KB 21.7 KB | Display Display | EMDB header |
Images | emd_17720.png | 125.9 KB | ||
Masks | emd_17720_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-17720.cif.gz | 4 KB | ||
Others | emd_17720_additional_1.map.gz emd_17720_half_map_1.map.gz emd_17720_half_map_2.map.gz | 212.4 MB 391 MB 390.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17720 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17720 | HTTPS FTP |
-Validation report
Summary document | emd_17720_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_17720_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_17720_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | emd_17720_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17720 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17720 | HTTPS FTP |
-Related structure data
Related structure data | 8qsjMC 8pk0C 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_17720.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_17720_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: full map, unsharpened
File | emd_17720_additional_1.map | ||||||||||||
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Annotation | full map, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17720_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17720_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,...
Entire | Name: large mitoribosomal subunit biogenesis intermediate with GTPBP10, GTPBP7, NSUN4-MTERF4, ACP-module |
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Components |
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-Supramolecule #1: large mitoribosomal subunit biogenesis intermediate with GTPBP10,...
Supramolecule | Name: large mitoribosomal subunit biogenesis intermediate with GTPBP10, GTPBP7, NSUN4-MTERF4, ACP-module type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#58 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.9 MDa |
-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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68901 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |