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Yorodumi- PDB-7nsh: 39S mammalian mitochondrial large ribosomal subunit with mtRRF (p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nsh | |||||||||
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Title | 39S mammalian mitochondrial large ribosomal subunit with mtRRF (post) and mtEFG2 | |||||||||
Components |
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Keywords | TRANSLATION / Ribosome / Mitochondria | |||||||||
Function / homology | Function and homology information Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation termination / Mitochondrial protein degradation ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation termination / Mitochondrial protein degradation / ribosome disassembly / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / ribosomal large subunit binding / organelle membrane / RNA processing / rescue of stalled ribosome / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / double-stranded RNA binding / cell junction / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / 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 / synapse / nucleolus / GTP binding / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Kummer, E. / Schubert, K. / Ban, N. | |||||||||
Funding support | Switzerland, 2items
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Citation | Journal: Mol Cell / Year: 2021 Title: Structural basis of translation termination, rescue, and recycling in mammalian mitochondria. Authors: Eva Kummer / Katharina Noel Schubert / Tanja Schoenhut / Alain Scaiola / Nenad Ban / Abstract: The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as ...The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process. | |||||||||
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 | 7nsh.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7nsh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nsh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nsh_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7nsh_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7nsh_validation.xml.gz | 244.4 KB | Display | |
Data in CIF | 7nsh_validation.cif.gz | 404.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/7nsh ftp://data.pdbj.org/pub/pdb/validation_reports/ns/7nsh | HTTPS FTP |
-Related structure data
Related structure data | 12567MC 7nqhC 7nqlC 7nsiC 7nsjC 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 ribosomal protein ... , 26 types, 32 molecules B0BaB8BbBcBdBeBgBiBjBmBnBtBxCLDLELFLGLHLLLB1B2B7BFBIBJBKBSBTBUBV
+Protein , 25 types, 25 molecules BYBfBhBlBoBpBqBuBvB9B3B4B5B6BCBDBGBQBEBNBOBPBRBWBX
-39S ribosomal protein ... , 2 types, 2 molecules BkBw
#14: Protein | Mass: 29942.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480J9Z6 |
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#24: Protein | Mass: 49100.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480QIM3 |
-RNA chain , 2 types, 2 molecules BABB
#29: RNA chain | Mass: 504852.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 33320725 |
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#36: RNA chain | Mass: 23402.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 76262549 |
-Non-polymers , 6 types, 231 molecules
#56: Chemical | ChemComp-MG / #57: Chemical | #58: Chemical | #59: Chemical | #60: Chemical | ChemComp-GNP / | #61: Water | ChemComp-HOH / | |
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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 |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
-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 FIELD |
Image recording | Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224731 / Symmetry type: POINT |