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Yorodumi- PDB-7nql: 55S mammalian mitochondrial ribosome with ICT1 and P site tRNAMet -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nql | |||||||||
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Title | 55S mammalian mitochondrial ribosome with ICT1 and P site tRNAMet | |||||||||
Components |
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Keywords | TRANSLATION / Ribosome / Mitochondria / ICT1 / TERMINATION | |||||||||
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 / : / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly ...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 translational termination / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / 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 / mitochondrial inner 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 | Sus scrofa (pig) Homo sapiens (human) unidentified (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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 | 7nql.cif.gz | 3.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7nql.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/7nql ftp://data.pdbj.org/pub/pdb/validation_reports/nq/7nql | HTTPS FTP |
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-Related structure data
Related structure data | 12529MC 7nqhC 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 ... , 40 types, 45 molecules B7B8BFBIBJBKBSBTBUBVBaBbBcBdBeBgBiBjBmBnBtBxCLDLELFLGLHLABAC...
+Protein , 38 types, 38 molecules B9BDBEBLBNBOBPBQBRBWBXBYBfBhBlBoBpBqBuBvAFAIAKAOAQAUAbAfAgAi...
-RNA chain , 5 types, 5 molecules BABBAAAVAX
#4: RNA chain | Mass: 504852.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig) / References: GenBank: 33320725 |
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#5: RNA chain | Mass: 23402.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig) / References: GenBank: 76262549 |
#47: RNA chain | Mass: 308989.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig) / References: GenBank: 11055671 |
#64: RNA chain | Mass: 22664.498 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: GenBank: 1208989970 |
#65: RNA chain | Mass: 1923.237 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-39S ribosomal protein ... , 2 types, 2 molecules BkBw
#35: Protein | Mass: 29942.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: MRPL48 / Production host: Sus scrofa (pig) / References: UniProt: A0A480J9Z6 |
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#45: Protein | Mass: 49100.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: MRPS30 / Production host: Sus scrofa (pig) / References: UniProt: A0A480QIM3 |
-28S ribosomal protein ... , 2 types, 2 molecules APAp
#60: Protein | Mass: 15182.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: MRPS16 / Production host: Sus scrofa (pig) / References: UniProt: A0A480JTD7 |
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#81: Protein | Mass: 29220.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: MRPS18B / Production host: Sus scrofa (pig) / References: UniProt: Q767K8 |
-Protein/peptide , 1 types, 1 molecules AZ
#66: Protein/peptide | Mass: 1297.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unidentified (others) |
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-Non-polymers , 6 types, 350 molecules
#89: Chemical | ChemComp-ZN / #90: Chemical | ChemComp-MG / #91: Chemical | #92: Chemical | #93: Chemical | ChemComp-GTP / | #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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93623 / Symmetry type: POINT |