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Open data
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Basic information
Entry | Database: PDB / ID: 8oir | ||||||||||||
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Title | 55S human mitochondrial ribosome with mtRF1 and P-site tRNA | ||||||||||||
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![]() | RIBOSOME / human mitochondrial ribosome / release factor mtRF1 / non-canonical stop codon | ||||||||||||
Function / homology | ![]() translation release factor activity / mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / translation release factor activity, codon specific ...translation release factor activity / mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / translation release factor activity, codon specific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / fibrillar center / 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 / endonuclease activity / cell population proliferation / mitochondrial inner membrane / tRNA binding / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / protein domain specific binding / intracellular membrane-bounded organelle / nucleotide binding / mRNA binding / synapse / nucleolus / GTP binding / apoptotic process / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
![]() | Saurer, M. / Leibundgut, M. / Scaiola, A. / Schoenhut, T. / Ban, N. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of translation termination at noncanonical stop codons in human mitochondria. Authors: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / ...Authors: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / David Gatfield / Aleksandra Filipovska / Nenad Ban / ![]() ![]() ![]() Abstract: The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the ...The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 4.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 16897MC ![]() 8oinC ![]() 8oipC ![]() 8oiqC ![]() 8oisC ![]() 8oitC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
+39S ribosomal protein ... , 48 types, 53 molecules B1B2B3B4B5B6BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBX...
-RNA chain , 6 types, 6 molecules B7B8B9AAAGAI
#2: RNA chain | Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: RNA chain | Mass: 500727.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: NCBI Reference Sequence: NC_012920.1 added 3' GU (encoded on genome but not annotated as part of the 16S rRNA), N1437>U as in MT079070.1 Source: (natural) ![]() |
#4: RNA chain | Mass: 22989.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: NCBI Reference Sequence: NC_012920.1 + aminoacylated CCA-end Source: (natural) ![]() |
#56: RNA chain | Mass: 306547.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: NCBI Reference Sequence: NC_012920.1 + one C at 3'-end (encoded but not annotated as part of the sequence), a A103>G and A791>G as found in e.g. GenBank: OM714795.1 Source: (natural) ![]() |
#62: RNA chain | Mass: 22692.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: NCBI Reference Sequence: NC_012920.1 + aminoacylated CCA-end Source: (natural) ![]() |
#64: RNA chain | Mass: 7329.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence as observed in the cryo-EM density map. / Source: (natural) ![]() |
-Protein , 8 types, 8 molecules BeBfBgBsADAaAcAe
#35: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#36: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#37: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#48: Protein | Mass: 23352.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#59: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#82: Protein | Mass: 56258.391 Da / Num. of mol.: 1 / Mutation: 311GGQ313 > AAQ Source method: isolated from a genetically manipulated source Details: Human mitochondrial release factor 1 (mtRF1), containing a 311GGQ>AAQ mutation, a C-terminal linker (GGSGGSGGSGGSGGSGG) and a 3xFLAG-tag (DYKDHDGDYKDHDIDYKDDDDK), expressed from a pcDNA3.1(+) ...Details: Human mitochondrial release factor 1 (mtRF1), containing a 311GGQ>AAQ mutation, a C-terminal linker (GGSGGSGGSGGSGGSGG) and a 3xFLAG-tag (DYKDHDGDYKDHDIDYKDDDDK), expressed from a pcDNA3.1(+) plasmid in HEK293 EBNA cells. Source: (gene. exp.) ![]() ![]() |
#84: Protein | Mass: 13540.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#86: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+28S ribosomal protein ... , 27 types, 27 molecules ABACAEAFAHAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAbAdAgAiAj
-Non-polymers , 9 types, 418 molecules ![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FS2.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FS2.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
#90: Chemical | ChemComp-K / #91: Chemical | ChemComp-MG / #92: Chemical | ChemComp-VAL / | #93: Chemical | #94: Chemical | #95: Chemical | ChemComp-MET / | #96: Chemical | ChemComp-ATP / | #97: Chemical | ChemComp-GDP / | #98: 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 human mitochondrial ribosome with mtRF1 and P-site tRNA Type: RIBOSOME Details: 55S human mitochondrial ribosome in complex with mtRF1(AAQ)-3xFLAG, human methionine-tRNA(Met), and an mRNA containing a non-canonical stop codon, purified from HEK293 EBNA cells. Entity ID: #1-#47, #49-#89 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight |
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Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Affinity-purified 55S mitoribosome. | ||||||||||||||||||||||||||||||
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 |
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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 / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 43882 |
EM imaging optics | Energyfilter slit width: 20 eV |
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Processing
EM software |
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Image processing | Details: Micrographs were motion corrected and CTF parameters were estimated using Cryosparc. | ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5423665 Details: Particles were picked with blob picker in Cryosparc. | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41288 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1
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