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Yorodumi- EMDB-18461: mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18461 | |||||||||
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Title | mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2 | |||||||||
Map data | mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2 | |||||||||
Sample |
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Keywords | Mitochondria / Assembly / GTPBP8 / RIBOSOME | |||||||||
Function / homology | Function and homology information negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / 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 ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / 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 / mitochondrial translational termination / mitochondrial translational elongation / 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 / mitochondrial large ribosomal subunit binding / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / [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 / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / double-stranded RNA binding / small ribosomal subunit rRNA binding / cell junction / large ribosomal subunit rRNA 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 / mRNA binding / nucleotide binding / calcium ion binding / synapse / 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: 2.42 Å | |||||||||
Authors | Valentin Gese G / Cipullo M / Rorbach J / Hallberg BM | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: GTPBP8 plays a role in mitoribosome formation in human mitochondria. Authors: Miriam Cipullo / Genís Valentín Gesé / Shreekara Gopalakrishna / Annika Krueger / Vivian Lobo / Maria A Pirozhkova / James Marks / Petra Páleníková / Dmitrii Shiriaev / Yong Liu / ...Authors: Miriam Cipullo / Genís Valentín Gesé / Shreekara Gopalakrishna / Annika Krueger / Vivian Lobo / Maria A Pirozhkova / James Marks / Petra Páleníková / Dmitrii Shiriaev / Yong Liu / Jelena Misic / Yu Cai / Minh Duc Nguyen / Abubakar Abdelbagi / Xinping Li / Michal Minczuk / Markus Hafner / Daniel Benhalevy / Aishe A Sarshad / Ilian Atanassov / B Martin Hällberg / Joanna Rorbach / Abstract: Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these ...Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these factors, GTP-binding proteins (GTPBPs) play important roles. In bacterial systems, numerous GTPBPs are required for ribosome subunit maturation, with EngB being a GTPBP involved in the ribosomal large subunit assembly. In this study, we focus on exploring the function of GTPBP8, the human homolog of EngB. We find that ablation of GTPBP8 leads to the inhibition of mitochondrial translation, resulting in significant impairment of oxidative phosphorylation. Structural analysis of mitoribosomes from GTPBP8 knock-out cells shows the accumulation of mitoribosomal large subunit assembly intermediates that are incapable of forming functional monosomes. Furthermore, fPAR-CLIP analysis reveals that GTPBP8 is an RNA-binding protein that interacts specifically with the mitochondrial ribosome large subunit 16 S rRNA. Our study highlights the role of GTPBP8 as a component of the mitochondrial gene expression machinery involved in mitochondrial large subunit maturation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18461.map.gz | 775.9 MB | EMDB map data format | |
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Header (meta data) | emd-18461-v30.xml emd-18461.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18461_fsc.xml | 19.6 KB | Display | FSC data file |
Images | emd_18461.png | 113.7 KB | ||
Masks | emd_18461_msk_1.map | 824 MB | Mask map | |
Filedesc metadata | emd-18461.cif.gz | 4.2 KB | ||
Others | emd_18461_half_map_1.map.gz emd_18461_half_map_2.map.gz | 763.4 MB 763.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18461 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18461 | HTTPS FTP |
-Validation report
Summary document | emd_18461_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_18461_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_18461_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | emd_18461_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18461 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18461 | HTTPS FTP |
-Related structure data
Related structure data | 8qu5MC 8qrkC 8qrlC 8qrmC 8qrnC 8qu1C 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_18461.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.01 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18461_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: mt-LSU assembly intermediate in GTPBP8 knock-out cells, state...
File | emd_18461_half_map_1.map | ||||||||||||
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Annotation | mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2, half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: mt-LSU assembly intermediate in GTPBP8 knock-out cells, state...
File | emd_18461_half_map_2.map | ||||||||||||
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Annotation | mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2, half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2
Entire | Name: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2 |
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Components |
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-Supramolecule #1: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2
Supramolecule | Name: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.7 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |