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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2676 | |||||||||
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Title | Electron cryo-microscopy of bovine ComplexI | |||||||||
![]() | Reconstruction of bovine ComplexI | |||||||||
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![]() | NADH dehydrogenase / respiratory complex | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.95 Å | |||||||||
![]() | Vinothkumar KR / Zhu J / Hirst J | |||||||||
![]() | ![]() Title: Architecture of mammalian respiratory complex I. Authors: Kutti R Vinothkumar / Jiapeng Zhu / Judy Hirst / ![]() Abstract: Complex I (NADH:ubiquinone oxidoreductase) is essential for oxidative phosphorylation in mammalian mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across ...Complex I (NADH:ubiquinone oxidoreductase) is essential for oxidative phosphorylation in mammalian mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the energy-transducing inner membrane, providing electrons for respiration and driving ATP synthesis. Mammalian complex I contains 44 different nuclear- and mitochondrial-encoded subunits, with a combined mass of 1 MDa. The 14 conserved 'core' subunits have been structurally defined in the minimal, bacterial complex, but the structures and arrangement of the 30 'supernumerary' subunits are unknown. Here we describe a 5 Å resolution structure of complex I from Bos taurus heart mitochondria, a close relative of the human enzyme, determined by single-particle electron cryo-microscopy. We present the structures of the mammalian core subunits that contain eight iron-sulphur clusters and 60 transmembrane helices, identify 18 supernumerary transmembrane helices, and assign and model 14 supernumerary subunits. Thus, we considerably advance knowledge of the structure of mammalian complex I and the architecture of its supernumerary ensemble around the core domains. Our structure provides insights into the roles of the supernumerary subunits in regulation, assembly and homeostasis, and a basis for understanding the effects of mutations that cause a diverse range of human diseases. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 78.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.2 KB 10.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.1 KB | Display | ![]() |
Images | ![]() | 377.5 KB | ||
Others | ![]() ![]() | 65.5 MB 65.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 329.4 KB | Display | ![]() |
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Full document | ![]() | 328.6 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uq8MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of bovine ComplexI | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.717 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 2676 half map 1.map
File | emd_2676_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 2676 half map 2.map
File | emd_2676_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : NADH:ubiquinone oxidoreductase
Entire | Name: NADH:ubiquinone oxidoreductase |
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Components |
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-Supramolecule #1000: NADH:ubiquinone oxidoreductase
Supramolecule | Name: NADH:ubiquinone oxidoreductase / type: sample / ID: 1000 Details: The enzyme was isolated from bovine heart mitochondria in detergent micelles and imaged on ice as single particles Oligomeric state: 1 / Number unique components: 1 |
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Molecular weight | Experimental: 1 MDa / Theoretical: 1 MDa |
-Macromolecule #1: NADH:ubiquinone oxidoreductase
Macromolecule | Name: NADH:ubiquinone oxidoreductase / type: protein_or_peptide / ID: 1 / Name.synonym: Complex I / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 1 MDa / 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 | 3.5 mg/mL |
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Buffer | pH: 8 / Details: 20mM Tris-HCl, 150 mM NaCl, 0.03% Cymal-7 |
Grid | Details: 300 mesh holey-carbon Quantifoil gold grid R 0.6/1 glow discharged in air |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: OTHER Method: The specimen was vitrified in an environmental plunge-freeze apparatus (Bellare et al, J.Electr. Micros. Tech., 1988, 10, 87-111). Blot for 15-18 seconds after the diameter of the blotted ...Method: The specimen was vitrified in an environmental plunge-freeze apparatus (Bellare et al, J.Electr. Micros. Tech., 1988, 10, 87-111). Blot for 15-18 seconds after the diameter of the blotted meniscus ceases to expand and plunged. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80 K / Max: 90 K / Average: 85 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification once at the start of data collection |
Details | Exposure intensity set to give 50 electron/pixel/second at the detector, which translates to ~17 electrons/square_Angstrom/second at the specimen. Each image was exposed for 4 seconds. |
Date | Oct 21, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 1154 / Average electron dose: 64 e/Å2 Details: An in-house built system was used to intercept the frames from the detector at a rate of 18 frames per second. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 81495 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |