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Yorodumi- PDB-7nqh: 55S mammalian mitochondrial ribosome with mtRF1a and P-site tRNAMet -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nqh | |||||||||
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Title | 55S mammalian mitochondrial ribosome with mtRF1a and P-site tRNAMet | |||||||||
Components |
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Keywords | TRANSLATION / Ribosome / Mitochondria / Termination / mtRF1a / Release | |||||||||
Function / homology | Function and homology information 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 / : / translation release factor activity / mitochondrial translational termination / mitochondrial transcription ...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 / : / translation release factor activity / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation termination / ribonuclease III activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / organelle membrane / RNA processing / rescue of stalled ribosome / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / double-stranded RNA binding / large ribosomal subunit / regulation of translation / cell junction / small ribosomal subunit / nuclear membrane / negative regulation of translation / rRNA binding / nuclear body / ribosome / mitochondrial matrix / structural constituent of ribosome / cell cycle / ribonucleoprotein complex / translation / protein domain specific binding / nucleotide binding / mRNA binding / intracellular membrane-bounded organelle / synapse / apoptotic process / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 | 7nqh.cif.gz | 3.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7nqh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/7nqh ftp://data.pdbj.org/pub/pdb/validation_reports/nq/7nqh | HTTPS FTP |
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-Related structure data
Related structure data | 12527MC 7nqlC 7nshC 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 ... , 38 types, 43 molecules CLDLELFLGLHLB0B1B2BFBIBJBKBSBTBUBVBaBbBcBeBgBiBjBmBnBtBxB7AB...
-RNA chain , 5 types, 5 molecules BBAAAVAXBA
#5: 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 |
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#48: RNA chain | Mass: 308989.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 11055671 |
#68: RNA chain | Mass: 22664.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1208989970 |
#69: RNA chain | Mass: 2839.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#88: 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 |
+Protein , 39 types, 39 molecules BDBEBLBNBOBPBQBRBWBXBYB3BdBfBhBlBoBpBqBuBvB4B5B6AFAIAKAOAQAU...
-39S ribosomal protein ... , 2 types, 2 molecules BkBw
#36: 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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#46: Protein | Mass: 49100.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480QIM3 |
-28S ribosomal protein ... , 3 types, 3 molecules AGAPAp
#57: Protein | Mass: 27778.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJ25 |
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#64: Protein | Mass: 15182.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JTD7 |
#86: Protein | Mass: 29220.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q767K8 |
-Protein/peptide , 1 types, 1 molecules AZ
#70: 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) Sus scrofa (pig) |
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-Non-polymers , 6 types, 338 molecules
#89: Chemical | ChemComp-MG / #90: Chemical | ChemComp-ZN / #91: Chemical | #92: Chemical | ChemComp-GTP / | #93: Chemical | #94: 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 |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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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 FIELDBright-field microscopy |
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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47048 / Symmetry type: POINT |