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Yorodumi- PDB-7a5i: Structure of the human mitoribosome with A- P-and E-site mt-tRNAs -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a5i | ||||||||||||
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Title | Structure of the human mitoribosome with A- P-and E-site mt-tRNAs | ||||||||||||
Components |
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Keywords | RIBOSOME / mitochondrial ribosome / ribosome stalling / cryo-EM | ||||||||||||
Function / homology | Function and homology information mitochondrial ribosome binding / mitochondrial translational termination / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation ...mitochondrial ribosome binding / mitochondrial translational termination / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / 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 / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / small ribosomal subunit rRNA binding / fibrillar center / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / double-stranded RNA binding / large ribosomal subunit / regulation of translation / cell junction / small ribosomal subunit / endonuclease activity / nuclear membrane / mitochondrial inner membrane / cell population proliferation / tRNA binding / 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 / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Desai, N. / Yang, H. / Chandrasekaran, V. / Kazi, R. / Minczuk, M. / Ramakrishnan, V. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Science / Year: 2020 Title: Elongational stalling activates mitoribosome-associated quality control. Authors: Nirupa Desai / Hanting Yang / Viswanathan Chandrasekaran / Razina Kazi / Michal Minczuk / V Ramakrishnan / Abstract: The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a ...The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a mitoribosome-associated quality control pathway that responds to interruptions during elongation, and we present structures at 3.1- to 3.3-angstrom resolution of mitoribosomal large subunits trapped during ribosome rescue. Release factor homolog C12orf65 (mtRF-R) and RNA binding protein C6orf203 (MTRES1) eject the nascent chain and peptidyl transfer RNA (tRNA), respectively, from stalled ribosomes. Recruitment of mitoribosome biogenesis factors to these quality control intermediates suggests additional roles for these factors during mitoribosome rescue. We also report related cryo-electron microscopy structures (3.7 to 4.4 angstrom resolution) of elongating mitoribosomes bound to tRNAs, nascent polypeptides, the guanosine triphosphatase elongation factors mtEF-Tu and mtEF-G1, and the Oxa1L translocase. | ||||||||||||
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 | 7a5i.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7a5i.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7a5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/7a5i ftp://data.pdbj.org/pub/pdb/validation_reports/a5/7a5i | HTTPS FTP |
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-Related structure data
Related structure data | 11644MC 7a5fC 7a5gC 7a5hC 7a5jC 7a5kC 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
-Protein/peptide , 2 types, 3 molecules Y2t3A5
#1: Protein/peptide | Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#54: Protein/peptide | Mass: 2400.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-RNA chain , 5 types, 7 molecules A3B3A6i49994X
#2: RNA chain | Mass: 500019.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1025814679 |
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#3: RNA chain | Mass: 23266.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#85: RNA chain | Mass: 306135.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#86: RNA chain | Mass: 2903.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#87: RNA chain | Mass: 23378.979 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
+39S ribosomal protein ... , 45 types, 45 molecules D3E3F3H3I3J3K3L3M3N3O3Q3R3S3T3U3V3W3X3Y3Z3031323334353637383...
-Protein , 8 types, 8 molecules P3j3o3p3q3c6d6e6
#15: Protein | Mass: 20465.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A8K9D2 |
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#45: Protein | Mass: 13696.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A8K7J6 |
#49: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
#50: 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 |
#51: 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: 13498.819 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 |
+28S ribosomal protein ... , 27 types, 27 molecules B6C6D6E6F6G6H6I6J6K6L6M6N6O6P6Q6R6S6T6U6V6W6X6Y6Z6a6b6
-Non-polymers , 4 types, 136 molecules
#88: Chemical | ChemComp-MG / #89: Chemical | ChemComp-ZN / #90: Chemical | ChemComp-CL / | #91: Chemical | ChemComp-GDP / | |
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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 mitoribosomeMitochondrial ribosome / Type: RIBOSOME / Entity ID: #1-#87 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.4 mg/ml / 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software | Name: EPU / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37415 / Symmetry type: POINT |