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Open data
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Basic information
Entry | Database: PDB / ID: 7pkt | |||||||||||||||
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Title | Large subunit of the Chlamydomonas reinhardtii mitoribosome | |||||||||||||||
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![]() | RIBOSOME / Mitochondria / mitoribosome / alga | |||||||||||||||
Function / homology | ![]() regulation of mitochondrial mRNA stability / chloroplast rRNA processing / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosome assembly / chloroplast / ribosomal large subunit assembly ...regulation of mitochondrial mRNA stability / chloroplast rRNA processing / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosome assembly / chloroplast / ribosomal large subunit assembly / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / mRNA binding / mitochondrion / RNA binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||||||||
![]() | Waltz, F. / Soufari, H. / Hashem, Y. | |||||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: How to build a ribosome from RNA fragments in Chlamydomonas mitochondria. Authors: Florent Waltz / Thalia Salinas-Giegé / Robert Englmeier / Herrade Meichel / Heddy Soufari / Lauriane Kuhn / Stefan Pfeffer / Friedrich Förster / Benjamin D Engel / Philippe Giegé / ...Authors: Florent Waltz / Thalia Salinas-Giegé / Robert Englmeier / Herrade Meichel / Heddy Soufari / Lauriane Kuhn / Stefan Pfeffer / Friedrich Förster / Benjamin D Engel / Philippe Giegé / Laurence Drouard / Yaser Hashem / ![]() ![]() ![]() Abstract: Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the ...Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green alga Chlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Additional proteins, mainly OPR, PPR and mTERF helical repeat proteins, are found in Chlamydomonas mitoribosome, revealing the structure of an OPR protein in complex with its RNA binding partner. Targeted amiRNA silencing indicates that these ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the inner mitochondrial membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of mitoribosome diversity and the various strategies these specialized molecular machines adopt for membrane tethering. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.3 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 | ![]() | 219.3 KB | Display | |
Data in CIF | ![]() | 369.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 13480MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
+Protein , 34 types, 34 molecules abcdjklpqstuvwxyABeDEFIJKLMNOP...
-50S ribosomal protein ... , 2 types, 2 molecules fo
#5: Protein | Mass: 30622.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#12: Protein | Mass: 13140.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Mitochondrial ribosomal protein ... , 6 types, 6 molecules imnrzG
#6: Protein | Mass: 29714.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#10: Protein | Mass: 21380.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The protein is a mixture of A0A2K3DXS2 and A8JH49,The protein is a mixture of A0A2K3DXS2 and A8JH49 Source: (natural) ![]() ![]() |
#11: Protein | Mass: 33412.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 25593.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 6864.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#30: Protein | Mass: 27320.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein/peptide , 3 types, 3 molecules CXZ
#35: Protein/peptide | Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#43: Protein/peptide | Mass: 2656.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#45: Protein/peptide | Mass: 4188.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain , 9 types, 9 molecules 120345678
#46: RNA chain | Mass: 51976.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#47: RNA chain | Mass: 27512.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#48: RNA chain | Mass: 24033.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#49: RNA chain | Mass: 59395.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#50: RNA chain | Mass: 38253.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#51: RNA chain | Mass: 47720.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#52: RNA chain | Mass: 43923.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#53: RNA chain | Mass: 186482.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#54: RNA chain | Mass: 132907.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 3 types, 71 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FES.gif)
#55: Chemical | ChemComp-ZN / | ||
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#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-FES / | |
-Details
Has 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 |
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Sample preparation
Component | Name: Large subunit of the mitochondrial ribosome of Chlamydomonas reinhardtii Type: RIBOSOME / Entity ID: #1-#54 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
Image scans | Movie frames/image: 65 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101291 / Num. of class averages: 2 / Symmetry type: POINT |