+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15937 | |||||||||
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Title | Drosophila melanogaster complex I in the Twisted state (Dm2) | |||||||||
Map data | Globally sharpened consensus map generated using RELION Postprocess | |||||||||
Sample |
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Keywords | Mitochondrial complex I / Respiratory complex I / NADH:ubiquinone oxidoreductase / Ubiquinone / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information Mitochondrial protein import / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / Protein lipoylation / Mitochondrial protein degradation / regulation of terminal button organization / Neutrophil degranulation / mitochondrial [2Fe-2S] assembly complex ...Mitochondrial protein import / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / Protein lipoylation / Mitochondrial protein degradation / regulation of terminal button organization / Neutrophil degranulation / mitochondrial [2Fe-2S] assembly complex / cellular respiration / ubiquinone binding / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / respiratory chain complex I / : / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / : / aerobic respiration / respiratory electron transport chain / proton transmembrane transport / reactive oxygen species metabolic process / determination of adult lifespan / response to reactive oxygen species / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / mitochondrion / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.68 Å | |||||||||
Authors | Agip ANA / Chung I / Sanchez-Martinez A / Whitworth AJ / Hirst J | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Elife / Year: 2023 Title: Cryo-EM structures of mitochondrial respiratory complex I from . Authors: Ahmed-Noor A Agip / Injae Chung / Alvaro Sanchez-Martinez / Alexander J Whitworth / Judy Hirst / Abstract: Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. is a ...Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. is a candidate model organism for complex I due to its high evolutionary conservation with the mammalian enzyme, well-developed genetic toolkit, and complex physiology for studies in specific cell types and tissues. Here, we isolate complex I from and determine its structure, revealing a 43-subunit assembly with high structural homology to its 45-subunit mammalian counterpart, including a hitherto unknown homologue to subunit NDUFA3. The major conformational state of the enzyme is the mammalian-type 'ready-to-go' active resting state, with a fully ordered and enclosed ubiquinone-binding site, but a subtly altered global conformation related to changes in subunit ND6. The mammalian-type 'deactive' pronounced resting state is not observed: in two minor states, the ubiquinone-binding site is unchanged, but a deactive-type π-bulge is present in ND6-TMH3. Our detailed structural knowledge of complex I provides a foundation for new approaches to disentangle mechanisms of complex I catalysis and regulation in bioenergetics and physiology. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15937.map.gz | 318 MB | EMDB map data format | |
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Header (meta data) | emd-15937-v30.xml emd-15937.xml | 67.9 KB 67.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15937_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_15937.png | 114.9 KB | ||
Masks | emd_15937_msk_1.map | 347.6 MB | Mask map | |
Filedesc metadata | emd-15937.cif.gz | 14.3 KB | ||
Others | emd_15937_additional_1.map.gz emd_15937_half_map_1.map.gz emd_15937_half_map_2.map.gz | 287.2 MB 279.5 MB 279.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15937 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15937 | HTTPS FTP |
-Validation report
Summary document | emd_15937_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_15937_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_15937_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | emd_15937_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15937 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15937 | HTTPS FTP |
-Related structure data
Related structure data | 8ba0MC 8b9zC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15937.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Globally sharpened consensus map generated using RELION Postprocess | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.048 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15937_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened and unfiltered consensus map generated using RELION...
File | emd_15937_additional_1.map | ||||||||||||
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Annotation | Unsharpened and unfiltered consensus map generated using RELION Postprocess | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 generated using RELION Postprocess (unsharpened...
File | emd_15937_half_map_1.map | ||||||||||||
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Annotation | Half map 1 generated using RELION Postprocess (unsharpened and unfiltered) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 generated using RELION Postprocess (unsharpened...
File | emd_15937_half_map_2.map | ||||||||||||
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Annotation | Half map 2 generated using RELION Postprocess (unsharpened and unfiltered) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mitochondrial respiratory complex I
+Supramolecule #1: Mitochondrial respiratory complex I
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #2: LD31474p
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #4: Complex I-49kD
+Macromolecule #5: NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A
+Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #7: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #9: NADH dehydrogenase (ubiquinone) 23 kDa subunit
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #14: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #16: NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A
+Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #19: Acyl carrier protein, mitochondrial
+Macromolecule #20: NADH dehydrogenase (Ubiquinone) 13 kDa B subunit
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #26: RH45008p
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #28: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #33: GEO11417p1
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #42: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #43: IRON/SULFUR CLUSTER
+Macromolecule #44: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #45: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #46: FLAVIN MONONUCLEOTIDE
+Macromolecule #47: CARDIOLIPIN
+Macromolecule #48: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #49: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #50: ZINC ION
+Macromolecule #51: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.4 mg/mL | ||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: UltrAuFoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. Details: Following glow discharge for 90 s at 20 mA, the grid was treated for 7 days in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ...Details: Following glow discharge for 90 s at 20 mA, the grid was treated for 7 days in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ethanol and dried prior to blotting | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 10 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3082 / Average exposure time: 10.0 sec. / Average electron dose: 41.88 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |