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Open data
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Basic information
Entry | Database: PDB / ID: 7nsj | |||||||||
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Title | 55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*) | |||||||||
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![]() | TRANSLATION / Ribosome / Mitochondria / tRNA(E*) | |||||||||
Function / homology | ![]() Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / : / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation ...Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / : / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / organelle membrane / positive regulation of proteolysis / ribosomal small subunit binding / RNA processing / rescue of stalled ribosome / double-stranded RNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / nuclear membrane / cytosolic small ribosomal subunit / 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 / mRNA binding / apoptotic process / synapse / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Kummer, E. / Schubert, K. / Ban, N. | |||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.9 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 | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 362.1 KB | Display | |
Data in CIF | ![]() | 600.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12569MC ![]() 7nqhC ![]() 7nqlC ![]() 7nshC ![]() 7nsiC 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
+Mitochondrial ribosomal protein ... , 38 types, 43 molecules B0B1B2B7BFBIBJBKBSBTBUBVBaBbBcBdBeBgB8BiBjBmBnBtBxABACAGAJAL...
+Protein , 37 types, 37 molecules B3B4B5B6BDBEBNBOBPBQBRBWBXBYBfBhBlBoBpBqBuBvB9AFAIAKAOAQAUAb...
-RNA chain , 5 types, 6 molecules BBAABAAVAYAX
#8: RNA chain | Mass: 23402.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
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#51: RNA chain | Mass: 308989.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
#53: RNA chain | Mass: 504852.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
#86: RNA chain | Mass: 21713.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #87: RNA chain | | Mass: 1792.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-39S ribosomal protein ... , 2 types, 2 molecules BkBw
#39: Protein | Mass: 29942.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#49: Protein | Mass: 49100.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-28S ribosomal protein ... , 4 types, 4 molecules AEAPAhAp
#56: Protein | Mass: 48213.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#65: Protein | Mass: 15182.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#77: Protein | Mass: 44091.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#84: Protein | Mass: 29220.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules AZ
#69: Protein/peptide | Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: unknown polypeptide modeled as poly-alanine / Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 338 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/HOH.gif)
#88: Chemical | ChemComp-MG / #89: Chemical | ChemComp-ZN / #90: Chemical | #91: Chemical | ChemComp-5GP / | #92: Chemical | ChemComp-GTP / | #93: Water | ChemComp-HOH / | |
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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 mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*) Type: RIBOSOME / Entity ID: #1-#87 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
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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 |
Image recording | Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26001 / Symmetry type: POINT |