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Yorodumi- PDB-6zm5: Human mitochondrial ribosome in complex with OXA1L, mRNA, A/A tRN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zm5 | |||||||||
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Title | Human mitochondrial ribosome in complex with OXA1L, mRNA, A/A tRNA, P/P tRNA and nascent polypeptide | |||||||||
Components |
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Keywords | RIBOSOME / mitochondrion / translation / membrane insertion / translocon / peptidyl-tRNA | |||||||||
Function / homology | Function and homology information mitochondrial protein quality control / protein insertion into mitochondrial inner membrane from matrix / membrane insertase activity / negative regulation of oxidoreductase activity / mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly ...mitochondrial protein quality control / protein insertion into mitochondrial inner membrane from matrix / membrane insertase activity / negative regulation of oxidoreductase activity / mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / negative regulation of ATP-dependent activity / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial proton-transporting ATP synthase complex assembly / 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 respiratory chain complex I assembly / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / Mitochondrial protein degradation / apoptotic signaling pathway / protein tetramerization / mitochondrial membrane / aerobic respiration / fibrillar center / cell junction / double-stranded RNA binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / cell population proliferation / tRNA binding / nuclear body / rRNA binding / negative regulation of translation / mitochondrial inner membrane / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleotide binding / synapse / positive regulation of DNA-templated transcription / nucleolus / GTP binding / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | |||||||||
Model details | Ribosome small subunit with initiation factors | |||||||||
Authors | Itoh, Y. / Andrell, J. / Amunts, A. | |||||||||
Funding support | Sweden, 1items
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Citation | Journal: Science / Year: 2021 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zm5.cif.gz | 6.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6zm5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zm5_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6zm5_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6zm5_validation.xml.gz | 305.4 KB | Display | |
Data in CIF | 6zm5_validation.cif.gz | 564.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/6zm5 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/6zm5 | HTTPS FTP |
-Related structure data
Related structure data | 11278MC 6zm6C 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
-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 / Source: (natural) Homo sapiens (human) / References: GenBank: 1563835895 |
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#2: RNA chain | Mass: 22961.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#54: RNA chain | Mass: 306120.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1858624182 |
#87: RNA chain | Mass: 21682.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Mixture of any mitochondrial tRNAs. Each residue was assigned as either A, U, G, or C, based on the density and conservation. Source: (natural) Homo sapiens (human) |
#88: RNA chain | Mass: 22369.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Mixture of any mitochondrial tRNAs. Each residue was assigned as either A, U, G, or C, based on the density and conservation. Source: (natural) Homo sapiens (human) |
#89: RNA chain | Mass: 6003.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Mixture of any mitochondrial mRNAs. Each residue was assigned as either A, U, G, or C, based on the density and conservation. Source: (natural) Homo sapiens (human) |
+39S ribosomal protein ... , 48 types, 53 molecules DEFHIJKLMNOPQRSTUVWXYZ01234567...
-Protein , 7 types, 7 molecules opqA2A3A4u
#48: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
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#49: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197, peptidyl-tRNA hydrolase |
#50: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8 |
#82: Protein | Mass: 13409.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BP2 |
#83: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWT8 |
#84: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY7 |
#85: Protein | Mass: 48602.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15070 |
+28S ribosomal protein ... , 27 types, 27 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZA0A1
-Protein/peptide , 1 types, 1 molecules v
#86: Protein/peptide | Mass: 2292.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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-Non-polymers , 8 types, 712 molecules
#90: Chemical | ChemComp-MG / #91: Chemical | ChemComp-K / #92: Chemical | #93: Chemical | #94: Chemical | ChemComp-ATP / | #95: Chemical | ChemComp-GTP / | #96: Chemical | ChemComp-ALA / | #97: 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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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 |
-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 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 |
-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: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30744 / 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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