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Yorodumi- EMDB-18440: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 3 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18440 | |||||||||
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Title | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 3 | |||||||||
Map data | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 3 | |||||||||
Sample |
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Keywords | Mitochondria / Assembly / GTPBP8 / RIBOSOME | |||||||||
Function / homology | Function and homology information mitochondrial translational initiation / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / ribosome disassembly / negative regulation of mitotic nuclear division ...mitochondrial translational initiation / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / ribosome disassembly / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / Mitochondrial protein degradation / translation initiation factor activity / apoptotic signaling pathway / fibrillar center / small ribosomal subunit rRNA binding / cell junction / ribosome binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / nuclear membrane / cell population proliferation / tRNA binding / mitochondrial inner membrane / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 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_18440.map.gz | 483.7 MB | EMDB map data format | |
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Header (meta data) | emd-18440-v30.xml emd-18440.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18440_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_18440.png | 51.1 KB | ||
Masks | emd_18440_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-18440.cif.gz | 4.2 KB | ||
Others | emd_18440_half_map_1.map.gz emd_18440_half_map_2.map.gz | 475.2 MB 475.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18440 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18440 | HTTPS FTP |
-Validation report
Summary document | emd_18440_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_18440_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_18440_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | emd_18440_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18440 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18440 | HTTPS FTP |
-Related structure data
Related structure data | 8qrmMC 8qrkC 8qrlC 8qrnC 8qu1C 8qu5C 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_18440.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 3 | ||||||||||||||||||||||||||||||||||||
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_18440_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state...
File | emd_18440_half_map_1.map | ||||||||||||
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Annotation | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 3, half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state...
File | emd_18440_half_map_2.map | ||||||||||||
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Annotation | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 3, 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 |