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Yorodumi- PDB-7odt: State C of the human mitoribosomal large subunit assembly intermediate -
+Open data
-Basic information
Entry | Database: PDB / ID: 7odt | ||||||||||||
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Title | State C of the human mitoribosomal large subunit assembly intermediate | ||||||||||||
Components |
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Keywords | RIBOSOME / mitoribosome / assembly intermediate / large subunit / LSU / mt-LSU | ||||||||||||
Function / homology | Function and homology information regulation of respiratory system process / tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation ...regulation of respiratory system process / tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / rRNA methyltransferase activity / Respiratory electron transport / iron-sulfur cluster assembly complex / mitochondrial translational termination / mitochondrial transcription / mitochondrial large ribosomal subunit binding / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / protein targeting to mitochondrion / [2Fe-2S] cluster assembly / Glyoxylate metabolism and glycine degradation / camera-type eye development / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / rRNA methylation / acyl binding / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / iron-sulfur cluster assembly / acyl carrier activity / mitochondrial translation / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ribosomal large subunit binding / anatomical structure morphogenesis / RNA processing / rescue of stalled ribosome / aerobic respiration / ribosomal large subunit biogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to leukemia inhibitory factor / methyltransferase activity / fatty acid binding / mitochondrial membrane / small ribosomal subunit rRNA binding / fibrillar center / rRNA processing / fatty acid biosynthetic process / large ribosomal subunit rRNA binding / double-stranded RNA binding / ribosome biogenesis / cell junction / heart development / 5S rRNA binding / double-stranded DNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / rRNA binding / nuclear body / ribosome / mitochondrial matrix / structural constituent of ribosome / cell cycle / translation / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / GTPase activity / synapse / apoptotic process / calcium ion binding / GTP binding / nucleolus / regulation of DNA-templated transcription / magnesium ion binding / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Lenarcic, T. / Jaskolowski, M. / Leibundgut, M. / Scaiola, A. / Schoenhut, T. / Saurer, M. / Lee, R.G. / Rackham, O. / Filipovska, A. / Ban, N. | ||||||||||||
Funding support | Switzerland, 3items
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Citation | Journal: Nat Commun / Year: 2021 Title: Stepwise maturation of the peptidyl transferase region of human mitoribosomes. Authors: Tea Lenarčič / Mateusz Jaskolowski / Marc Leibundgut / Alain Scaiola / Tanja Schönhut / Martin Saurer / Richard G Lee / Oliver Rackham / Aleksandra Filipovska / Nenad Ban / Abstract: Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral ...Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. The structural basis of the mammalian mitochondrial ribosome assembly is currently not well understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. We discover that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by the MRM2 methyltransferase and quality control interactions with the conserved mitochondrial GTPase MTG2 that contacts the sarcin-ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7odt.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7odt.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7odt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/7odt ftp://data.pdbj.org/pub/pdb/validation_reports/od/7odt | HTTPS FTP |
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-Related structure data
Related structure data | 12847MC 7odrC 7odsC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Mitochondrial ... , 3 types, 3 molecules tuB
#1: Protein | Mass: 44018.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293 EBNA / References: UniProt: Q9H4K7 |
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#2: Protein | Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293 EBNA / References: UniProt: Q96EH3 |
#18: RNA chain | Mass: 22961.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293 EBNA |
-Protein , 7 types, 7 molecules vwxyopq
#3: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293 EBNA / References: UniProt: L0R8F8 |
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#4: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293 EBNA / References: UniProt: O14561 |
#5: Protein | Mass: 43140.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293 EBNA References: UniProt: Q96CB9, Transferases; Transferring one-carbon groups; Methyltransferases |
#6: Protein | Mass: 44012.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293 EBNA / References: UniProt: Q7Z6M4 |
#54: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293 EBNA / References: UniProt: Q9BQC6 |
#55: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293 EBNA / References: UniProt: Q14197, peptidyl-tRNA hydrolase |
#56: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293 EBNA / References: UniProt: Q8TAE8 |
+39S ribosomal protein ... , 47 types, 47 molecules 0123456789DEFHIJKLMNOPQRSTUVWX...
-RNA chain , 1 types, 1 molecules A
#17: RNA chain | Mass: 500047.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293 EBNA |
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-Non-polymers , 7 types, 111 molecules
#59: Chemical | ChemComp-GDP / | ||||||||||
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#60: Chemical | ChemComp-MG / #61: Chemical | ChemComp-PM8 / | #62: Chemical | ChemComp-SAM / | #63: Chemical | #64: Chemical | ChemComp-K / #65: Chemical | ChemComp-FES / | |
-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: State C of the human mitoribosomal large subunit assembly intermediate Type: RIBOSOME / Entity ID: #1-#58 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) / Strain: HEK 293 EBNA | ||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: 4 uL of the sample was blotted for 2-6 sec before plunging |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
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: 62552 / Symmetry type: POINT |