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Yorodumi- PDB-7a5j: Structure of the split human mitoribosomal large subunit with P-a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a5j | ||||||||||||
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Title | Structure of the split human mitoribosomal large subunit with 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 negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport / mitochondrial translational termination ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport / mitochondrial translational termination / mitochondrial translational elongation / translation release factor activity, codon nonspecific / positive regulation of mitochondrial translation / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / [2Fe-2S] cluster assembly / aminoacyl-tRNA hydrolase activity / respiratory chain complex I / mitochondrial ribosome / iron-sulfur cluster assembly / mitochondrial translation / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / anatomical structure morphogenesis / acyl carrier activity / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / double-stranded RNA binding / large ribosomal subunit / small ribosomal subunit rRNA binding / cell junction / regulation of translation / large ribosomal subunit rRNA binding / 5S rRNA binding / endonuclease activity / tRNA binding / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / mRNA binding / nucleotide binding / calcium ion binding / synapse / nucleolus / apoptotic process / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Thermus thermophilus HB27 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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 | 7a5j.cif.gz | 2.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7a5j.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7a5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a5j_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7a5j_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7a5j_validation.xml.gz | 210.3 KB | Display | |
Data in CIF | 7a5j_validation.cif.gz | 376.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/7a5j ftp://data.pdbj.org/pub/pdb/validation_reports/a5/7a5j | HTTPS FTP |
-Related structure data
Related structure data | 11645MC 7a5fC 7a5gC 7a5hC 7a5iC 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
+39S ribosomal protein ... , 45 types, 46 molecules DEFHCIJKLMNOQRSTUVWXYZ01234567...
-Mitochondrial ... , 2 types, 2 molecules Pu
#12: 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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#52: Protein | Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EH3 |
-Protein , 7 types, 7 molecules jopqvwn
#42: Protein | Mass: 13696.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A8K7J6 |
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#46: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
#47: 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 |
#48: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8 |
#53: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8 |
#54: Protein | Mass: 17774.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561 |
#55: Protein | Mass: 24867.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72GV9 |
-Unknown protein/protein ... , 3 types, 3 molecules tyz
#51: Protein/peptide | Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#60: Protein/peptide | Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#61: Protein/peptide | Mass: 1209.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-RNA chain , 3 types, 4 molecules ABGx
#56: 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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#57: RNA chain | Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1485738021 |
#59: RNA chain | Mass: 23378.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-Protein/peptide , 1 types, 1 molecules Y2
#58: 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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-Non-polymers , 4 types, 101 molecules
#62: Chemical | ChemComp-MG / #63: Chemical | #64: Chemical | #65: Chemical | ChemComp-NA / |
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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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Source (natural) |
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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 FIELD |
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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54398 / Symmetry type: POINT |