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Yorodumi- PDB-6zse: Human mitochondrial ribosome in complex with mRNA, A/P-tRNA and P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zse | ||||||||||||||||||
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Title | Human mitochondrial ribosome in complex with mRNA, A/P-tRNA and P/E-tRNA | ||||||||||||||||||
Components |
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Keywords | TRANSLATION / Mitochondria / Ribosome / mRNA / tRNA | ||||||||||||||||||
Function / homology | Function and homology information 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 / Mitochondrial translation elongation / Mitochondrial translation termination ...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 / 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 / cytosolic small ribosomal subunit / endonuclease activity / cell population proliferation / cytosolic large ribosomal subunit / 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 / apoptotic process / nucleolus / GTP binding / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å | ||||||||||||||||||
Authors | Aibara, S. / Singh, V. / Modelska, A. / Amunts, A. | ||||||||||||||||||
Funding support | 4items
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Citation | Journal: Elife / Year: 2020 Title: Structural basis of mitochondrial translation. Authors: Shintaro Aibara / Vivek Singh / Angelika Modelska / Alexey Amunts / Abstract: Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the ...Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the binding of mt-mRNA and to what extent they are involved in the translocation of transfer RNA (mt-tRNA) is unclear. To visualize the process of translation in human mitochondria, we report ~3.0 Å resolution structure of the human mitoribosome, including the L7/L12 stalk, and eight structures of its functional complexes with mt-mRNA, mt-tRNAs, recycling factor and additional trans factors. The study reveals a transacting protein module LRPPRC-SLIRP that delivers mt-mRNA to the mitoribosomal small subunit through a dedicated platform formed by the mitochondria-specific protein mS39. Mitoribosomal proteins of the large subunit mL40, mL48, and mL64 coordinate translocation of mt-tRNA. The comparison between those structures shows dynamic interactions between the mitoribosome and its ligands, suggesting a sequential mechanism of conformational changes. | ||||||||||||||||||
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 | 6zse.cif.gz | 6.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6zse.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/6zse ftp://data.pdbj.org/pub/pdb/validation_reports/zs/6zse | HTTPS FTP |
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-Related structure data
Related structure data | 11395MC 6zs9C 6zsaC 6zsbC 6zscC 6zsdC 6zsgC 7og4C 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
+39S ribosomal protein ... , 48 types, 53 molecules 0123456789XDXEXFXHXIXJXKXLXMXNXOXPXQXRXSXTXUXVXWXX...
-RNA chain , 6 types, 6 molecules XAAAXBr1r2r3
#11: RNA chain | Mass: 500694.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
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#17: RNA chain | Mass: 296647.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#43: RNA chain | Mass: 22961.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#83: RNA chain | Mass: 3821.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#84: RNA chain | Mass: 22427.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#85: RNA chain | Mass: 21446.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
+28S ribosomal protein ... , 27 types, 27 molecules A0A1ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZ
-Protein , 6 types, 6 molecules A2A3A4opq
#14: Protein | Mass: 13498.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BP2 |
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#15: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWT8 |
#16: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY7 |
#79: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
#80: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197, peptidyl-tRNA hydrolase |
#81: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8 |
-Protein/peptide , 1 types, 1 molecules A
-Non-polymers , 4 types, 204 molecules
#89: Chemical | ChemComp-ZN / #90: Chemical | ChemComp-MG / #91: Chemical | ChemComp-DOL / | #92: Chemical | ChemComp-GTP / | |
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-Details
Compound details | QUINUPRISTHas 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 | Name: Human mitochondrial ribosome / Type: RIBOSOME / Entity ID: #1-#87 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4966 / Symmetry type: POINT |