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Open data
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Basic information
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Title | Matrix arm of active state CI from Rotenone dataset | ||||||||||||
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![]() | mammalian / mitochondrial / respiratory / complex I / ELECTRON TRANSPORT | ||||||||||||
Function / homology | ![]() RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Mitochondrial protein degradation / cardiac muscle tissue development / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / : ...RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Mitochondrial protein degradation / cardiac muscle tissue development / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / 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 / : / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / respiratory electron transport chain / reactive oxygen species metabolic process / electron transport chain / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / nuclear body / protein-containing complex binding / mitochondrion / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
![]() | Gu JK / Yang MJ | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The coupling mechanism of mammalian mitochondrial complex I. Authors: Jinke Gu / Tianya Liu / Runyu Guo / Laixing Zhang / Maojun Yang / ![]() Abstract: Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in ...Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in mitochondria. In the present study, we report cryo-electron microscopy structures of CI from Sus scrofa in six treatment conditions at a resolution of 2.4-3.5 Å, in which CI structures of each condition can be classified into two biochemical classes (active or deactive), with a notably higher proportion of active CI particles. These structures illuminate how hydrophobic ubiquinone-10 (Q10) with its long isoprenoid tail is bound and reduced in a narrow Q chamber comprising four different Q10-binding sites. Structural comparisons of active CI structures from our decylubiquinone-NADH and rotenone-NADH datasets reveal that Q10 reduction at site 1 is not coupled to proton pumping in the membrane arm, which might instead be coupled to Q10 oxidation at site 2. Our data overturn the widely accepted previous proposal about the coupling mechanism of CI. | ||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 10.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.8 KB 29.8 KB | Display Display | ![]() |
Images | ![]() | 76.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vyfMC ![]() 7v2cC ![]() 7v2dC ![]() 7v2eC ![]() 7v2fC ![]() 7v2hC ![]() 7v2kC ![]() 7v2rC ![]() 7v30C ![]() 7v31C ![]() 7v32C ![]() 7v33C ![]() 7v3mC ![]() 7vb7C ![]() 7vblC ![]() 7vbnC ![]() 7vbpC ![]() 7vbzC ![]() 7vc0C ![]() 7vwjC ![]() 7vwlC ![]() 7vxpC ![]() 7vxsC ![]() 7vxuC ![]() 7vy1C ![]() 7vy8C ![]() 7vy9C ![]() 7vyaC ![]() 7vyeC ![]() 7vygC ![]() 7vyhC ![]() 7vyiC ![]() 7vynC ![]() 7vysC ![]() 7vz1C ![]() 7vz8C ![]() 7vzvC ![]() 7vzwC ![]() 7w00C ![]() 7w0hC ![]() 7w0rC ![]() 7w0yC ![]() 7w1oC ![]() 7w1pC ![]() 7w1tC ![]() 7w1uC ![]() 7w1vC ![]() 7w1zC ![]() 7w20C ![]() 7w2kC ![]() 7w2lC ![]() 7w2rC ![]() 7w2uC ![]() 7w2yC ![]() 7w31C ![]() 7w32C ![]() 7w35C ![]() 7w4cC ![]() 7w4dC ![]() 7w4eC ![]() 7w4fC ![]() 7w4gC ![]() 7w4jC ![]() 7w4kC ![]() 7w4lC ![]() 7w4mC ![]() 7w4nC ![]() 7w4qC M: atomic model generated by this map C: citing same article ( |
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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: 1.0742 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Respiratory complex I
+Supramolecule #1: Respiratory complex I
+Macromolecule #1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #5: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #6: Acyl carrier protein, mitochondrial
+Macromolecule #7: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #8: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #9: NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitoc...
+Macromolecule #10: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #11: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #12: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #13: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #14: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #15: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #16: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #19: IRON/SULFUR CLUSTER
+Macromolecule #20: FLAVIN MONONUCLEOTIDE
+Macromolecule #21: (2R,6aS,12aS)-8,9-dimethoxy-2-(prop-1-en-2-yl)-1,2,12,12a-tetrahy...
+Macromolecule #22: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #23: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #24: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #25: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
+Macromolecule #26: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #27: MAGNESIUM ION
+Macromolecule #28: CARDIOLIPIN
+Macromolecule #29: ZINC ION
-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: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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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) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111024 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |