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- PDB-7o9m: Human mitochondrial ribosome large subunit assembly intermediate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o9m | |||||||||||||||||||||||||||
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Title | Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1 and the MALSU module | |||||||||||||||||||||||||||
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![]() | RIBOSOME / Mitochondria / GTPase / Ribosome assembly intermediate | |||||||||||||||||||||||||||
Function / homology | ![]() mRNA (cytidine-5-)-methyltransferase activity / regulation of respiratory system process / rRNA modification in the mitochondrion / mitochondrial RNA modification / mitochondrial RNA catabolic process / regulation of mitochondrial translation / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (uridine-2'-O-)-methyltransferase activity ...mRNA (cytidine-5-)-methyltransferase activity / regulation of respiratory system process / rRNA modification in the mitochondrion / mitochondrial RNA modification / mitochondrial RNA catabolic process / regulation of mitochondrial translation / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / protein lipoylation / Complex I biogenesis / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / positive regulation of mitochondrial translation / RNA methylation / Respiratory electron transport / rRNA methyltransferase activity / RNA methyltransferase activity / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / camera-type eye development / translation release factor activity / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit / iron-sulfur cluster assembly complex / mitochondrial fission / mitochondrial large ribosomal subunit binding / peptidyl-tRNA hydrolase / rRNA methylation / mitochondrial ribosome / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / mitochondrial translation / [2Fe-2S] cluster assembly / protein targeting to mitochondrion / iron-sulfur cluster assembly / acyl binding / acyl carrier activity / ribosomal large subunit binding / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / respiratory chain complex I / anatomical structure morphogenesis / RNA processing / rescue of stalled ribosome / Mitochondrial protein degradation / cellular response to leukemia inhibitory factor / aerobic respiration / Transferases; Transferring one-carbon groups; Methyltransferases / ribosomal large subunit biogenesis / fatty acid binding / methyltransferase activity / mitochondrial membrane / fibrillar center / rRNA processing / fatty acid biosynthetic process / cell junction / large ribosomal subunit / double-stranded RNA binding / heart development / double-stranded DNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / endonuclease activity / mitochondrial inner membrane / nuclear body / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / protein domain specific binding / translation / ribonucleoprotein complex / nucleotide binding / GTPase activity / mRNA binding / apoptotic process / calcium ion binding / regulation of DNA-templated transcription / GTP binding / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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 | ![]() | 2.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 232.8 KB | Display | |
Data in CIF | ![]() | 390.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12764MC ![]() 7o9kC 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
-RNA chain , 2 types, 2 molecules AB
#1: RNA chain | Mass: 500033.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: RNA chain | Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Mitochondrial ... , 3 types, 3 molecules CPu
#3: Protein | Mass: 37195.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#15: Protein | Mass: 20465.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#58: Protein | Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+39S ribosomal protein ... , 47 types, 52 molecules DEFHIJKLMNOQRSTUVWXYZa01234567...
-Protein , 8 types, 8 molecules opqnA1A2vw
#49: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#50: Protein | Mass: 23559.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#51: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#54: 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 |
#55: 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 |
#56: Protein | Mass: 44012.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#57: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#60: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide , 1 types, 1 molecules UNK
#61: Protein/peptide | Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 5 types, 109 molecules 








#62: Chemical | ChemComp-MG / #63: Chemical | ChemComp-GDP / | #64: Chemical | #65: Chemical | ChemComp-SAM / | #66: Chemical | ChemComp-PNS / | |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-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-#61 / 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: 48.2 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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48646 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5OOL Accession code: 5OOL / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2.6→2.6 Å / Cor.coef. Fo:Fc: 0.882 / WRfactor Rwork: 0.379 / SU B: 9.548 / SU ML: 0.184 / Average fsc overall: 0.6573 / Average fsc work: 0.6573 / ESU R: 0.244 / Details: Hydrogens have not been used
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Solvent computation | Solvent model: BABINET MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.038 Å2
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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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