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- PDB-7qh7: Cryo-EM structure of the human mtLSU assembly intermediate upon M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qh7 | ||||||
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Title | Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 4 | ||||||
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![]() | RIBOSOME / Mitochondria / Assembly / Methyltransferase / MRM2 / RNA modification | ||||||
Function / homology | ![]() negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial translational elongation / iron-sulfur cluster assembly complex ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial translational elongation / iron-sulfur cluster assembly complex / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial large ribosomal subunit binding / Glyoxylate metabolism and glycine degradation / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / [2Fe-2S] cluster assembly / mitochondrial small ribosomal subunit / iron-sulfur cluster assembly / mitochondrial ribosome / mitochondrial translation / ribosomal large subunit binding / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I assembly / acyl binding / acyl carrier activity / RNA processing / Mitochondrial protein degradation / aerobic respiration / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / fatty acid biosynthetic process / double-stranded RNA binding / small ribosomal subunit rRNA binding / 5S rRNA binding / endonuclease activity / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / nucleotide binding / mRNA binding / apoptotic process / calcium ion binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | ||||||
![]() | Rebelo-Guiomar, P. / Pellegrino, S. / Dent, K.C. / Warren, A.J. / Minczuk, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit. Authors: Pedro Rebelo-Guiomar / Simone Pellegrino / Kyle C Dent / Aldema Sas-Chen / Leonor Miller-Fleming / Caterina Garone / Lindsey Van Haute / Jack F Rogan / Adam Dinan / Andrew E Firth / Byron ...Authors: Pedro Rebelo-Guiomar / Simone Pellegrino / Kyle C Dent / Aldema Sas-Chen / Leonor Miller-Fleming / Caterina Garone / Lindsey Van Haute / Jack F Rogan / Adam Dinan / Andrew E Firth / Byron Andrews / Alexander J Whitworth / Schraga Schwartz / Alan J Warren / Michal Minczuk / ![]() ![]() ![]() Abstract: Many cellular processes, including ribosome biogenesis, are regulated through post-transcriptional RNA modifications. Here, a genome-wide analysis of the human mitochondrial transcriptome shows that ...Many cellular processes, including ribosome biogenesis, are regulated through post-transcriptional RNA modifications. Here, a genome-wide analysis of the human mitochondrial transcriptome shows that 2'-O-methylation is limited to residues of the mitoribosomal large subunit (mtLSU) 16S mt-rRNA, introduced by MRM1, MRM2 and MRM3, with the modifications installed by the latter two proteins being interdependent. MRM2 controls mitochondrial respiration by regulating mitoribosome biogenesis. In its absence, mtLSU particles (visualized by cryo-EM at the resolution of 2.6 Å) present disordered RNA domains, partial occupancy of bL36m and bound MALSU1:L0R8F8:mtACP anti-association module, allowing five mtLSU biogenesis intermediates with different intersubunit interface configurations to be placed along the assembly pathway. However, mitoribosome biogenesis does not depend on the methyltransferase activity of MRM2. Disruption of the MRM2 Drosophila melanogaster orthologue leads to mitochondria-related developmental arrest. This work identifies a key checkpoint during mtLSU assembly, essential to maintain mitochondrial homeostasis. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 930.4 KB | Display | ![]() |
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Full document | ![]() | 964.7 KB | Display | |
Data in XML | ![]() | 153.2 KB | Display | |
Data in CIF | ![]() | 250 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 13967MC ![]() 7qh6C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
+39S ribosomal protein ... , 41 types, 41 molecules DEFHIKLMNOPQRSTUVWXYZ01235679a...
-Protein , 6 types, 6 molecules opquvw
#39: Protein | Mass: 9768.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#40: Protein | Mass: 14901.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#41: Protein | Mass: 11942.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#44: Protein | Mass: 13280.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#45: Protein | Mass: 8329.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#46: Protein | Mass: 9144.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 2 types, 2 molecules AB
#47: RNA chain | Mass: 403061.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#48: RNA chain | Mass: 19530.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 3 types, 67 molecules ![](data/chem/img/MG.gif)
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#50: Chemical | ChemComp-MG / #51: Chemical | #52: Water | ChemComp-HOH / | |
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-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 |
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Sample preparation
Component | Name: Human mitochondrial ribosome large subunit / Type: RIBOSOME / Entity ID: #1-#49 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 52.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2709521 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224933 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5OOL |