+Open data
-Basic information
Entry | Database: PDB / ID: 7a24 | |||||||||
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Title | Assembly intermediate of the plant mitochondrial complex I | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Respiration / Complex I / mitochondria / plant | |||||||||
Function / homology | Function and homology information L-galactonolactone dehydrogenase / galactonolactone dehydrogenase activity / L-gulono-1,4-lactone dehydrogenase activity / D-arabinono-1,4-lactone oxidase activity / cold acclimation / NADH dehydrogenase complex / Lyases; Carbon-oxygen lyases; Hydro-lyases / photorespiration / embryo development ending in seed dormancy / plant-type vacuole ...L-galactonolactone dehydrogenase / galactonolactone dehydrogenase activity / L-gulono-1,4-lactone dehydrogenase activity / D-arabinono-1,4-lactone oxidase activity / cold acclimation / NADH dehydrogenase complex / Lyases; Carbon-oxygen lyases; Hydro-lyases / photorespiration / embryo development ending in seed dormancy / plant-type vacuole / L-ascorbic acid biosynthetic process / respiratory chain complex I / cobalt ion binding / response to osmotic stress / acyl carrier activity / plastid / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / protein homotrimerization / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / respiratory electron transport chain / FAD binding / chloroplast / mitochondrial membrane / carbonate dehydratase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / peroxisome / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / membrane => GO:0016020 / mitochondrial matrix / copper ion binding / nucleolus / mitochondrion / zinc ion binding / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Brassica oleracea (wild cabbage) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Soufari, H. / Waltz, F. / Hashem, Y. | |||||||||
Funding support | France, 2items
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Citation | Journal: Nat Commun / Year: 2020 Title: Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM. Authors: Heddy Soufari / Camila Parrot / Lauriane Kuhn / Florent Waltz / Yaser Hashem / Abstract: Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the ...Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the mitochondrial respiratory chain and constitutes the largest of the respiratory complexes. Its structure and composition vary across eukaryote species. However, high resolution structures are available only for one group of eukaryotes, opisthokonts. In plants, only biochemical studies were carried out, already hinting at the peculiar composition of complex I in the green lineage. Here, we report several cryo-electron microscopy structures of the plant mitochondrial complex I. We describe the structure and composition of the plant respiratory complex I, including the ancestral mitochondrial domain composed of the carbonic anhydrase. We show that the carbonic anhydrase is a heterotrimeric complex with only one conserved active site. This domain is crucial for the overall stability of complex I as well as a peculiar lipid complex composed of cardiolipin and phosphatidylinositols. Moreover, we also describe the structure of one of the plant-specific complex I assembly intermediates, lacking the whole P module, in presence of the maturation factor GLDH. GLDH prevents the binding of the plant specific P1 protein, responsible for the linkage of the P to the P module. | |||||||||
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 | 7a24.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7a24.ent.gz | 913.3 KB | Display | PDB format |
PDBx/mmJSON format | 7a24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/7a24 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/7a24 | HTTPS FTP |
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-Related structure data
Related structure data | 11615MC 7a23C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 32 types, 33 molecules AIJNHKYZVWSijGCTFBOPRUEDXcQkno...
-Protein/peptide , 1 types, 1 molecules r
#29: Protein/peptide | Mass: 1723.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) |
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-Non-polymers , 9 types, 17 molecules
#34: Chemical | ChemComp-SF4 / #35: Chemical | ChemComp-FMN / | #36: Chemical | #37: Chemical | ChemComp-CDL / | #38: Chemical | ChemComp-PEV / ( | #39: Chemical | #40: Chemical | ChemComp-NDP / | #41: Chemical | #42: Chemical | ChemComp-BCT / | |
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-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 |
-Sample preparation
Component | Name: Plant mitochondrial respiratory complex I assembly intermediate in presence of GLDH Type: COMPLEX / Entity ID: #1-#33 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Brassica oleracea (wild cabbage) / Organ: Flower / Organelle: Mitochondria |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36513 / Symmetry type: POINT |