+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11615 | |||||||||
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Title | Assembly intermediate of the plant mitochondrial complex I | |||||||||
Map data | test | |||||||||
Sample |
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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 / Lyases; Carbon-oxygen lyases; Hydro-lyases / NADH dehydrogenase complex / photorespiration / embryo development ending in seed dormancy / L-ascorbic acid biosynthetic process ...L-galactonolactone dehydrogenase / galactonolactone dehydrogenase activity / L-gulono-1,4-lactone dehydrogenase activity / D-arabinono-1,4-lactone oxidase activity / cold acclimation / Lyases; Carbon-oxygen lyases; Hydro-lyases / NADH dehydrogenase complex / photorespiration / embryo development ending in seed dormancy / L-ascorbic acid biosynthetic process / plant-type vacuole / respiratory chain complex I / response to osmotic stress / plastid / cobalt ion binding / NADH:ubiquinone reductase (H+-translocating) / protein homotrimerization / acyl carrier activity / quinone binding / : / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / FAD binding / chloroplast / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / carbonate dehydratase activity / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / transmembrane transport / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / FMN binding / peroxisome / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / mitochondrial inner membrane / mitochondrial matrix / copper ion binding / nucleolus / mitochondrion / zinc ion binding / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Brassica oleracea (wild cabbage) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Soufari H / Waltz F / Hashem Y | |||||||||
Funding support | France, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11615.map.gz | 162.7 MB | EMDB map data format | |
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Header (meta data) | emd-11615-v30.xml emd-11615.xml | 43.3 KB 43.3 KB | Display Display | EMDB header |
Images | emd_11615.png | 23.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11615 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11615 | HTTPS FTP |
-Validation report
Summary document | emd_11615_validation.pdf.gz | 292.3 KB | Display | EMDB validaton report |
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Full document | emd_11615_full_validation.pdf.gz | 291.5 KB | Display | |
Data in XML | emd_11615_validation.xml.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11615 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11615 | HTTPS FTP |
-Related structure data
Related structure data | 7a24MC 7a23C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11615.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | test | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Plant mitochondrial respiratory complex I assembly intermediate i...
+Supramolecule #1: Plant mitochondrial respiratory complex I assembly intermediate i...
+Macromolecule #1: 51kDa
+Macromolecule #2: Nad2m
+Macromolecule #3: Nad3m
+Macromolecule #4: Nad6m
+Macromolecule #5: Nad1m
+Macromolecule #6: Nad4Lm
+Macromolecule #7: PGIV
+Macromolecule #8: B16.6
+Macromolecule #9: MWFE
+Macromolecule #10: B9
+Macromolecule #11: B14.5a
+Macromolecule #12: B14.5b
+Macromolecule #13: 15kDa
+Macromolecule #14: Nad7m
+Macromolecule #15: 75kDa
+Macromolecule #16: 39kDa
+Macromolecule #17: Nad9m
+Macromolecule #18: 24kDa
+Macromolecule #19: 18kDa
+Macromolecule #20: 13kDa
+Macromolecule #21: B13
+Macromolecule #22: B17.2
+Macromolecule #23: PSST
+Macromolecule #24: TYKY
+Macromolecule #25: B14
+Macromolecule #26: MNLL
+Macromolecule #27: B8
+Macromolecule #28: ACPM1
+Macromolecule #29: Unk1
+Macromolecule #30: P2
+Macromolecule #31: CAL1
+Macromolecule #32: CA1
+Macromolecule #33: GLDH
+Macromolecule #34: IRON/SULFUR CLUSTER
+Macromolecule #35: FLAVIN MONONUCLEOTIDE
+Macromolecule #36: Phosphatidylinositol
+Macromolecule #37: CARDIOLIPIN
+Macromolecule #38: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...
+Macromolecule #39: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #40: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #41: ZINC ION
+Macromolecule #42: BICARBONATE ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 36513 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |