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- EMDB-14537: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Op... -
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Open data
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Basic information
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Title | Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open state | |||||||||
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![]() | Complex I / NADH / Quinone / PROTON TRANSPORT | |||||||||
Function / homology | ![]() NADH dehydrogenase (quinone) / NADH dehydrogenase complex / : / NADH:ubiquinone reductase (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / molybdopterin cofactor binding / respiratory chain complex I / ubiquinone binding / quinone binding ...NADH dehydrogenase (quinone) / NADH dehydrogenase complex / : / NADH:ubiquinone reductase (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / molybdopterin cofactor binding / respiratory chain complex I / ubiquinone binding / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Kravchuk V / Kampjut D / Sazanov L | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A universal coupling mechanism of respiratory complex I. Authors: Vladyslav Kravchuk / Olga Petrova / Domen Kampjut / Anna Wojciechowska-Bason / Zara Breese / Leonid Sazanov / ![]() ![]() ![]() Abstract: Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone ...Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a 'domino effect' series of proton transfers and electrostatic interactions: the forward wave ('dominoes stacking') primes the pump, and the reverse wave ('dominoes falling') results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 37 KB 37 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.8 KB | Display | ![]() |
Images | ![]() | 87.6 KB | ||
Filedesc metadata | ![]() | 9.9 KB | ||
Others | ![]() ![]() | 268.6 MB 266.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z7tMC ![]() 7p61C ![]() 7p62C ![]() 7p63C ![]() 7p64C ![]() 7p69C ![]() 7p7cC ![]() 7p7eC ![]() 7p7jC ![]() 7p7kC ![]() 7p7lC ![]() 7p7mC ![]() 7z7rC ![]() 7z7sC ![]() 7z7vC ![]() 7z80C ![]() 7z83C ![]() 7z84C ![]() 7zc5C ![]() 7zciC ![]() 7zd6C ![]() 7zdhC ![]() 7zdjC ![]() 7zdmC ![]() 7zdpC ![]() 7zebC 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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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: PA focused map
File | emd_14537_additional_1.map | ||||||||||||
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Annotation | PA focused map | ||||||||||||
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Density Histograms |
-Additional map: MD focused map
File | emd_14537_additional_2.map | ||||||||||||
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Annotation | MD focused map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Complex I
+Supramolecule #1: Complex I
+Macromolecule #1: NADH-quinone oxidoreductase subunit F
+Macromolecule #2: NADH dehydrogenase I subunit E
+Macromolecule #3: NADH-quinone oxidoreductase
+Macromolecule #4: NADH-quinone oxidoreductase subunit C/D
+Macromolecule #5: NADH-quinone oxidoreductase subunit B
+Macromolecule #6: NADH-quinone oxidoreductase subunit I
+Macromolecule #7: NADH-quinone oxidoreductase subunit J
+Macromolecule #8: NADH-quinone oxidoreductase subunit H
+Macromolecule #9: NADH-quinone oxidoreductase subunit A
+Macromolecule #10: NADH dehydrogenase subunit L
+Macromolecule #11: NADH dehydrogenase I subunit M
+Macromolecule #12: NADH-quinone oxidoreductase subunit N
+Macromolecule #13: NADH-quinone oxidoreductase subunit K
+Macromolecule #14: IRON/SULFUR CLUSTER
+Macromolecule #15: FLAVIN MONONUCLEOTIDE
+Macromolecule #16: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
+Macromolecule #17: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #18: CALCIUM ION
+Macromolecule #19: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #20: EICOSANE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.25 mg/mL | |||||||||||||||||||||||||||
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Buffer | pH: 6 Component:
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Grid | Model: Quantifoil R0.6/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.9 | |||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11316 / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 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: 81000 |
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 |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: ML | ||||||
Output model | ![]() PDB-7z7t: |