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- PDB-7o9k: Human mitochondrial ribosome large subunit assembly intermediate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o9k | ||||||
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Title | Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-Tu | ||||||
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![]() | RIBOSOME / Mitochondria / GTPase / Ribosome assembly intermediate | ||||||
Function / homology | ![]() regulation of respiratory system process / rRNA modification in the mitochondrion / SARS-CoV-2 modulates autophagy / regulation of mitochondrial translation / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / rRNA (uridine-2'-O-)-methyltransferase activity / negative regulation of ribosome biogenesis ...regulation of respiratory system process / rRNA modification in the mitochondrion / SARS-CoV-2 modulates autophagy / regulation of mitochondrial translation / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / rRNA (uridine-2'-O-)-methyltransferase activity / negative regulation of ribosome biogenesis / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / RNA methylation / rRNA methyltransferase activity / Respiratory electron transport / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / iron-sulfur cluster assembly complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / mitochondrial large ribosomal subunit binding / protein targeting to mitochondrion / Glyoxylate metabolism and glycine degradation / mitochondrial fission / camera-type eye development / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / [2Fe-2S] cluster assembly / mitochondrial small ribosomal subunit / rRNA methylation / aminoacyl-tRNA hydrolase activity / iron-sulfur cluster assembly / translational elongation / mitochondrial ribosome / mitochondrial translation / mitochondrial nucleoid / 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 / anatomical structure morphogenesis / acyl carrier activity / RNA processing / translation elongation factor activity / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / Transferases; Transferring one-carbon groups; Methyltransferases / ribosomal large subunit biogenesis / 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 / ribosome biogenesis / cell junction / heart development / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / double-stranded DNA binding / endonuclease activity / response to ethanol / mitochondrial outer membrane / 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 / GTPase activity / mRNA binding / apoptotic process / synapse / calcium ion binding / regulation of DNA-templated transcription / nucleolus / GTP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Valentin Gese, G. / Hallberg, B.M. | ||||||
![]() | ![]() Title: Structural basis for late maturation steps of the human mitoribosomal large subunit. Authors: Miriam Cipullo / Genís Valentín Gesé / Anas Khawaja / B Martin Hällberg / Joanna Rorbach / ![]() ![]() Abstract: Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. ...Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. Mitoribosome biogenesis follows distinct molecular pathways that remain poorly understood. Here, we determine the cryo-EM structures of mitoribosomes isolated from human cell lines with either depleted or overexpressed mitoribosome assembly factor GTPBP5, allowing us to capture consecutive steps during mitoribosomal large subunit (mt-LSU) biogenesis. Our structures provide essential insights into the last steps of 16S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, which require the coordinated action of nine assembly factors. We show that mammalian-specific MTERF4 contributes to the folding of 16S rRNA, allowing 16 S rRNA methylation by MRM2, while GTPBP5 and NSUN4 promote fine-tuning rRNA rearrangements leading to PTC formation. Moreover, our data reveal an unexpected involvement of the elongation factor mtEF-Tu in mt-LSU assembly, where mtEF-Tu interacts with GTPBP5, similar to its interaction with tRNA during translational elongation. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 225.4 KB | Display | |
Data in CIF | ![]() | 361.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12763MC ![]() 7o9mC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
+39S ribosomal protein ... , 47 types, 53 molecules 0a123456789DEFFFt1t2t3t4t5t6HIJKLMNOQ...
-RNA chain , 2 types, 2 molecules AB
#12: RNA chain | Mass: 500033.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#14: RNA chain | Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 9 types, 9 molecules A1A2nopqtvw
#13: Protein | Mass: 43140.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q96CB9, Transferases; Transferring one-carbon groups; Methyltransferases |
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#15: Protein | Mass: 44012.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#53: Protein | Mass: 27464.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q9UI43, Transferases; Transferring one-carbon groups; Methyltransferases |
#54: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#55: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#56: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#59: Protein | Mass: 49613.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#61: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#62: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Mitochondrial ... , 4 types, 4 molecules CGPu
#16: Protein | Mass: 37292.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#21: Protein | Mass: 45015.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#30: Protein | Mass: 20465.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#60: Protein | Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide , 1 types, 1 molecules UNK
#63: Protein/peptide | Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 7 types, 101 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/PNS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/PNS.gif)
#64: Chemical | #65: Chemical | ChemComp-MG / #66: Chemical | ChemComp-SAM / | #67: Chemical | #68: Chemical | ChemComp-GTP / | #69: Chemical | ChemComp-SAH / | #70: Chemical | ChemComp-PNS / | |
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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: 55S subunit assembly intermediate / Type: RIBOSOME Details: Assembly intermediate of the human mitochondrial ribosome large subunit Entity ID: #1-#63 / Source: NATURAL |
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Molecular weight | Value: 1.5 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 20 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 49.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV |
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Processing
Software | Name: REFMAC / Version: 5.8.0267 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39495 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5OOL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell | Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %
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