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- PDB-6zm6: Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zm6 | |||||||||
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Title | Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA | |||||||||
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![]() | RIBOSOME / mitochondrion / translation / closed nascent-polypeptide tunnel | |||||||||
Function / homology | ![]() mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / 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 / 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 / cytosolic small ribosomal subunit / endonuclease activity / cell population proliferation / cytosolic large ribosomal subunit / mitochondrial inner membrane / tRNA binding / 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 / intracellular membrane-bounded organelle / nucleotide binding / mRNA binding / apoptotic process / synapse / nucleolus / GTP binding / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å | |||||||||
Model details | Ribosome small subunit with initiation factors | |||||||||
![]() | Itoh, Y. / Andrell, J. / Amunts, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of membrane-tethered mitochondrial protein synthesis. Authors: Yuzuru Itoh / Juni Andréll / Austin Choi / Uwe Richter / Priyanka Maiti / Robert B Best / Antoni Barrientos / Brendan J Battersby / Alexey Amunts / ![]() ![]() ![]() ![]() Abstract: Mitochondrial ribosomes (mitoribosomes) are tethered to the mitochondrial inner membrane to facilitate the cotranslational membrane insertion of the synthesized proteins. We report cryo-electron ...Mitochondrial ribosomes (mitoribosomes) are tethered to the mitochondrial inner membrane to facilitate the cotranslational membrane insertion of the synthesized proteins. We report cryo-electron microscopy structures of human mitoribosomes with nascent polypeptide, bound to the insertase oxidase assembly 1-like (OXA1L) through three distinct contact sites. OXA1L binding is correlated with a series of conformational changes in the mitoribosomal large subunit that catalyze the delivery of newly synthesized polypeptides. The mechanism relies on the folding of mL45 inside the exit tunnel, forming two specific constriction sites that would limit helix formation of the nascent chain. A gap is formed between the exit and the membrane, making the newly synthesized proteins accessible. Our data elucidate the basis by which mitoribosomes interact with the OXA1L insertase to couple protein synthesis and membrane delivery. | |||||||||
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 | ![]() | 6.7 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1001.1 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 304.5 KB | Display | |
Data in CIF | ![]() | 563 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11279MC ![]() 6zm5C 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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Components
-RNA chain , 6 types, 6 molecules ABAAwxy
#1: RNA chain | Mass: 500671.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
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#2: RNA chain | Mass: 22961.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
#54: RNA chain | Mass: 306120.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
#85: RNA chain | Mass: 21682.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
#86: RNA chain | Mass: 22369.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
#87: RNA chain | Mass: 6003.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
+39S ribosomal protein ... , 48 types, 53 molecules DEFHIJKLMNOPQRSTUVWXYZ01234567...
-Protein , 6 types, 6 molecules opqA2A3A4
#48: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
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#49: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
#50: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
#82: Protein | Mass: 13409.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
#83: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
#84: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
+28S ribosomal protein ... , 27 types, 27 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZA0A1
-Non-polymers , 7 types, 711 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/HOH.gif)
#88: Chemical | ChemComp-MG / #89: Chemical | ChemComp-K / #90: Chemical | #91: Chemical | #92: Chemical | ChemComp-ATP / | #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 |
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Sample preparation
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Molecular weight |
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Source (natural) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: 165000 X / Calibrated defocus min: 200 nm / Calibrated defocus max: 3600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 19655 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 20 / Used frames/image: 1-20 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1308158 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93615 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 44 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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