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Yorodumi- PDB-7a5f: Structure of the stalled human mitoribosome with P- and E-site mt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a5f | ||||||||||||
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Title | Structure of the stalled human mitoribosome 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 mitochondrial ribosome binding / rRNA import into mitochondrion / 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 ribosome binding / rRNA import into mitochondrion / 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 / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / Mitochondrial protein degradation / apoptotic signaling pathway / 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 / cytosolic large ribosomal subunit / 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 / nucleolus / GTP binding / apoptotic process / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Thermus thermophilus (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 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 | 7a5f.cif.gz | 3.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7a5f.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7a5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a5f_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7a5f_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7a5f_validation.xml.gz | 318.7 KB | Display | |
Data in CIF | 7a5f_validation.cif.gz | 571.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/7a5f ftp://data.pdbj.org/pub/pdb/validation_reports/a5/7a5f | HTTPS FTP |
-Related structure data
Related structure data | 11641MC 7a5gC 7a5hC 7a5iC 7a5jC 7a5kC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10809 (Title: Single particle cryo-EM of human mitochondrial ribosomes from Pde12 KO cells Data size: 45.7 TB Data #1: 7 independent datasets in TIF format from Titan Krios + Falcon III integrating mode [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein/peptide , 2 types, 2 molecules Y2A5
#1: Protein/peptide | Mass: 2079.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#53: Protein/peptide | Mass: 2008.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-RNA chain , 5 types, 6 molecules A3B3A624Ci4
#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: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1485738021 | ||
#84: RNA chain | Mass: 306135.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) | ||
#85: RNA chain | Mass: 23378.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #86: RNA chain | | Mass: 3240.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
+39S ribosomal protein ... , 47 types, 49 molecules D3E3F3H3DI3J3K3L3M3N3O3P3Q3R3S3T3U3V3W3X3Y3Z303132333435363...
-Protein , 7 types, 7 molecules o3p3q3c6d6e6n
#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 |
#81: Protein | Mass: 13498.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BP2 |
#82: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWT8 |
#83: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY7 |
#88: Protein | Mass: 24867.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72GV9 |
+28S ribosomal protein ... , 27 types, 27 molecules B6C6D6E6F6G6H6I6J6K6L6M6N6O6P6Q6R6S6T6U6V6W6X6Y6Z6a6b6
-Non-polymers , 8 types, 225 molecules
#89: Chemical | ChemComp-MG / #90: Chemical | ChemComp-ZN / #91: Chemical | ChemComp-GDP / | #92: Chemical | ChemComp-SO4 / | #93: Chemical | #94: Chemical | #95: Chemical | ChemComp-NA / #96: Water | ChemComp-HOH / | |
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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
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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 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16588 / Symmetry type: POINT |