+Open data
-Basic information
Entry | Database: PDB / ID: 8qrl | ||||||
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Title | mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2 | ||||||
Components |
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Keywords | RIBOSOME / Mitochondria / Assembly / GTPBP8 | ||||||
Function / homology | Function and homology information rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial ribosome binding / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / rRNA base methylation / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit ...rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial ribosome binding / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / rRNA base methylation / 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 / Transferases; Transferring one-carbon groups; Methyltransferases / apoptotic signaling pathway / small ribosomal subunit rRNA binding / cell junction / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å | ||||||
Authors | Valentin Gese, G. / Cipullo, M. / Rorbach, J. / Hallberg, B.M. | ||||||
Funding support | 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qrl.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8qrl.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 8qrl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qrl_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8qrl_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8qrl_validation.xml.gz | 173 KB | Display | |
Data in CIF | 8qrl_validation.cif.gz | 285.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/8qrl ftp://data.pdbj.org/pub/pdb/validation_reports/qr/8qrl | HTTPS FTP |
-Related structure data
Related structure data | 18439MC 8qrkC 8qrmC 8qrnC 8qu1C 8qu5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 306547.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: GenBank: OM714795.1 |
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+28S ribosomal protein ... , 27 types, 27 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ01
-Protein , 3 types, 3 molecules 348
#29: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9NWT8 |
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#30: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q96EY7 |
#31: Protein | Mass: 46184.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL15, METT5D1 / Production host: Homo sapiens (human) References: UniProt: A6NJ78, Transferases; Transferring one-carbon groups; Methyltransferases |
-Non-polymers , 9 types, 2239 molecules
#32: Chemical | ChemComp-NAD / | ||||||||||||||
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#33: Chemical | ChemComp-MG / #34: Chemical | ChemComp-K / #35: Chemical | ChemComp-ZN / | #36: Chemical | #37: Chemical | ChemComp-ATP / | #38: Chemical | ChemComp-GDP / | #39: Chemical | ChemComp-SAH / | #40: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: mtSSU assembly intermediate (State 2) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#31 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
EM embedding | Material: Ice |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 200 nm |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 435172 |
3D reconstruction | Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32577 / Symmetry type: POINT |