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Open data
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Basic information
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Title | Drosophila melanogaster complex I in the Cracked state (Dm3) | |||||||||
![]() | Globally sharpened consensus map generated using RELION Postprocess | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.96 Å | |||||||||
![]() | Agip AA / Chung I / Sanchez-Martinez A / Whitworth AJ / Hirst J | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 317.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.5 KB 24.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.9 KB | Display | ![]() |
Images | ![]() | 84 KB | ||
Masks | ![]() | 347.6 MB | ![]() | |
Others | ![]() ![]() ![]() | 287.4 MB 279.6 MB 279.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1003 KB | Display | ![]() |
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Full document | ![]() | 1002.6 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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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
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Density Histograms |
-Additional map: Unsharpened and unfiltered consensus map generated using RELION...
File | emd_15938_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 2 generated using RELION Postprocess (unsharpened...
File | emd_15938_half_map_1.map | ||||||||||||
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Annotation | Half map 2 generated using RELION Postprocess (unsharpened and unfiltered) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 generated using RELION Postprocess (unsharpened...
File | emd_15938_half_map_2.map | ||||||||||||
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Annotation | Half map 1 generated using RELION Postprocess (unsharpened and unfiltered) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Mitochondrial respiratory complex I
Entire | Name: Mitochondrial respiratory complex I |
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Components |
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-Supramolecule #1: Mitochondrial respiratory complex I
Supramolecule | Name: Mitochondrial respiratory complex I / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#43 Details: Native purification of mitochondrial complex I from Drosophila melanogaster (fruit fly) W1118. |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 1 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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. |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL |