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- PDB-7of7: Structure of a human mitochondrial ribosome large subunit assembl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7of7 | ||||||||||||||||||
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Title | Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset1). | ||||||||||||||||||
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![]() | RIBOSOME / Mitochondria / Biogenesis / GTPase / NSUN4 / MTERF4 | ||||||||||||||||||
Function / homology | ![]() regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / protein lipoylation ...regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / 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 / 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 / anatomical structure morphogenesis / acyl carrier activity / RNA processing / 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 / 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 / magnesium 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: 2.5 Å | ||||||||||||||||||
![]() | Hillen, H.S. / Lavdovskaia, E. / Nadler, F. / Hanitsch, E. / Linden, A. / Bohnsack, K.E. / Urlaub, H. / Richter-Dennerlein, R. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling. Authors: Hauke S Hillen / Elena Lavdovskaia / Franziska Nadler / Elisa Hanitsch / Andreas Linden / Katherine E Bohnsack / Henning Urlaub / Ricarda Richter-Dennerlein / ![]() Abstract: Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by ...Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by conserved GTPases, but the molecular basis is poorly understood. Here, we define the mechanism of GTPase-driven maturation of the human mitochondrial large ribosomal subunit (mtLSU) using endogenous complex purification, in vitro reconstitution and cryo-EM. Structures of transient native mtLSU assembly intermediates that accumulate in GTPBP6-deficient cells reveal how the biogenesis factors GTPBP5, MTERF4 and NSUN4 facilitate PTC folding. Addition of recombinant GTPBP6 reconstitutes late mtLSU biogenesis in vitro and shows that GTPBP6 triggers a molecular switch and progression to a near-mature PTC state. Additionally, cryo-EM analysis of GTPBP6-treated mature mitochondrial ribosomes reveals the structural basis for the dual-role of GTPBP6 in ribosome biogenesis and recycling. Together, these results provide a framework for understanding step-wise PTC folding as a critical conserved quality control checkpoint. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 183.2 KB | Display | |
Data in CIF | ![]() | 298 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12872MC ![]() 7of0C ![]() 7of2C ![]() 7of3C ![]() 7of4C ![]() 7of5C ![]() 7of6C 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 ... , 46 types, 46 molecules 0123456789DEFHIJKLMNOPQRSTUVWX...
-RNA chain , 1 types, 1 molecules A
#11: RNA chain | Mass: 500061.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Mitochondrial ... , 3 types, 3 molecules Bux
#12: RNA chain | Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#54: Protein | Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#57: Protein | Mass: 44018.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 7 types, 7 molecules CGopqvw
#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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#17: Protein | Mass: 44012.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#49: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#50: Protein | Mass: 23674.203 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) ![]() |
#55: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#56: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 2 types, 77 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#58: Chemical | #59: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | Y |
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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 assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset1). Type: RIBOSOME / Entity ID: #1-#57 / 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 type: Quantifoil R3.5/1 |
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 magnification: 81000 X / Calibrated defocus min: 300 nm / Calibrated defocus max: 2800 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 36 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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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: 9378438 | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98227 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5OOL |