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- EMDB-28581: Structure of mitochondrial complex I from Drosophila melanogaster... -
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Open data
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Basic information
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Title | Structure of mitochondrial complex I from Drosophila melanogaster, Flexible-class 1 | |||||||||
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Function / homology | ![]() Mitochondrial protein import / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / NADH dehydrogenase / Mitochondrial protein degradation / regulation of terminal button organization / Neutrophil degranulation ...Mitochondrial protein import / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / NADH dehydrogenase / Mitochondrial protein degradation / regulation of terminal button organization / Neutrophil degranulation / protein lipoylation / deoxynucleoside kinase activity / cellular respiration / ubiquinone-6 biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / : / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / determination of adult lifespan / response to reactive oxygen species / mitochondrial membrane / mitochondrial intermembrane space / transmembrane transport / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial matrix / protein-containing complex binding / mitochondrion / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Padavannil A / Letts JA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Resting mitochondrial complex I from adopts a helix-locked state. Authors: Abhilash Padavannil / Anjaneyulu Murari / Shauna-Kay Rhooms / Edward Owusu-Ansah / James A Letts / ![]() Abstract: Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the ...Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the evolutionary split between Protostomia and Deuterostomia. Complex I from Deuterostomia including mammals can adopt a biochemically defined off-pathway 'deactive' state, whereas complex I from Protostomia cannot. The presence of off-pathway states complicates the interpretation of structural results and has led to considerable mechanistic debate. Here, we report the structure of mitochondrial complex I from the thoracic muscles of the model protostome . We show that although complex I (-CI) does not have a NEM-sensitive deactive state, it does show slow activation kinetics indicative of an off-pathway resting state. The resting-state structure of -CI from the thoracic muscle reveals multiple conformations. We identify a helix-locked state in which an N-terminal α-helix on the NDUFS4 subunit wedges between the peripheral and membrane arms. Comparison of the -CI structure and conformational states to those observed in bacteria, yeast, and mammals provides insight into the roles of subunits across organisms, explains why the -CI off-pathway resting state is NEM insensitive, and raises questions regarding current mechanistic models of complex I turnover. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 484 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 57.7 KB 57.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.9 KB | Display | ![]() |
Images | ![]() | 36.8 KB | ||
Others | ![]() ![]() | 474.4 MB 474.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8eswMC ![]() 8eszC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_28581_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28581_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : mitochondrial complex I from the thoracic muscles of D. melanogaster
+Supramolecule #1: mitochondrial complex I from the thoracic muscles of D. melanogaster
+Macromolecule #1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #3: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #5: NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A
+Macromolecule #6: LD31474p
+Macromolecule #7: NADH dehydrogenase (ubiquinone) 23 kDa subunit
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #9: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #12: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #13: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #14: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #15: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #17: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #20: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #26: Acyl carrier protein, mitochondrial
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #29: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #30: NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A
+Macromolecule #31: GEO11417p1
+Macromolecule #32: Complex I-49kD
+Macromolecule #33: NADH dehydrogenase [ubiquinone] flavoprotein 3
+Macromolecule #34: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #35: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #36: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #37: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #39: NADH dehydrogenase (Ubiquinone) 13 kDa B subunit
+Macromolecule #40: RH45008p
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #43: CARDIOLIPIN
+Macromolecule #44: ZINC ION
+Macromolecule #45: IRON/SULFUR CLUSTER
+Macromolecule #46: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #47: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #48: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #49: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #50: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #51: FLAVIN MONONUCLEOTIDE
+Macromolecule #52: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | ![]() PDB-8esw: |