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- PDB-7a5k: Structure of the human mitoribosome in the post translocation sta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7a5k | ||||||||||||
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Title | Structure of the human mitoribosome in the post translocation state bound to mtEF-G1 | ||||||||||||
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![]() | RIBOSOME / mitochondrial ribosome / ribosome stalling / cryo-EM | ||||||||||||
Function / homology | ![]() protein insertion into mitochondrial inner membrane from matrix / membrane insertase activity / negative regulation of oxidoreductase activity / mitochondrial ribosome binding / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / microprocessor complex / negative regulation of ATP-dependent activity / translation release factor activity, codon nonspecific ...protein insertion into mitochondrial inner membrane from matrix / membrane insertase activity / negative regulation of oxidoreductase activity / mitochondrial ribosome binding / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / 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 / mitochondrial respiratory chain complex I assembly / anatomical structure morphogenesis / RNA processing / translation elongation factor activity / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / mitochondrial membrane / apoptotic signaling pathway / protein tetramerization / 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 / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / intracellular membrane-bounded organelle / nucleotide binding / GTPase activity / mRNA binding / apoptotic process / synapse / nucleolus / GTP binding / protein homodimerization activity / protein-containing complex / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
![]() | Desai, N. / Yang, H. / Chandrasekaran, V. / Kazi, R. / Minczuk, M. / Ramakrishnan, V. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.9 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 337.5 KB | Display | |
Data in CIF | ![]() | 602 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11646MC ![]() 7a5fC ![]() 7a5gC ![]() 7a5hC ![]() 7a5iC ![]() 7a5jC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.889641061155, 0.143494096409, -0.433529960444), (0.00216523401307, 0.948012435547, 0.318225916306), (0.456655333997, -0.284045535686, 0.843080090851)Vector: 38. ...NCS oper: (Code: given Matrix: (0.889641061155, 0.143494096409, -0.433529960444), Vector: |
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Components
-Protein , 8 types, 8 molecules r1j3o3p3q3c6d6e6
#1: Protein | Mass: 83578.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#45: Protein | Mass: 13696.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#49: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#50: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#51: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#83: Protein | Mass: 13498.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#84: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#85: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide , 2 types, 2 molecules Y2B
#2: Protein/peptide | Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#90: Protein/peptide | Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 5 types, 7 molecules A38B3u3A624FE
#3: RNA chain | Mass: 500019.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: RNA chain | | Mass: 23266.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #54: RNA chain | | Mass: 589.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #86: RNA chain | | Mass: 306135.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #87: RNA chain | Mass: 23378.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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+39S ribosomal protein ... , 46 types, 47 molecules D3E3F3H3DI3J3K3L3M3N3O3Q3R3S3T3U3V3W3X3Y3Z30313233343536373...
-Mitochondrial ... , 2 types, 2 molecules P3A5
#16: Protein | Mass: 20465.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#55: Protein | Mass: 48602.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+28S ribosomal protein ... , 27 types, 27 molecules B6C6D6E6F6G6H6I6J6K6L6M6N6O6P6Q6R6S6T6U6V6W6X6Y6Z6a6b6
-Non-polymers , 5 types, 138 molecules ![](data/chem/img/GCP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GDP.gif)
#91: Chemical | ChemComp-GCP / | ||||||
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#92: Chemical | ChemComp-MG / #93: Chemical | ChemComp-SPD / | #94: Chemical | ChemComp-ZN / #95: Chemical | ChemComp-GDP / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: human mitoribosome / Type: RIBOSOME / Entity ID: #1-#89 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
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 |
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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: ![]() |
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) |
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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: 19767 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.61 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS | Type: NCS constraints / Rms dev position: 0.000697267250097 Å |