+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32267 | ||||||||||||
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Title | Active state CI from DQ-NADH dataset, Subclass 3 | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information Mitochondrial protein import / RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / Mitochondrial protein degradation / oxidoreductase activity, acting on NAD(P)H / cardiac muscle tissue development / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity ...Mitochondrial protein import / RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / Mitochondrial protein degradation / oxidoreductase activity, acting on NAD(P)H / cardiac muscle tissue development / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / respiratory chain complex I / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / negative regulation of intrinsic apoptotic signaling pathway / ATP synthesis coupled electron transport / quinone binding / : / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / electron transport chain / negative regulation of cell growth / mitochondrial intermembrane space / 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 / nuclear speck / mitochondrial matrix / endoplasmic reticulum / mitochondrion / nucleoplasm / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) / pig (pig) / Pig (pig) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||
Authors | Gu JK / Yang MJ | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 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. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32267.map.gz | 15.4 MB | EMDB map data format | |
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Header (meta data) | emd-32267-v30.xml emd-32267.xml | 55.5 KB 55.5 KB | Display Display | EMDB header |
Images | emd_32267.png | 82.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32267 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32267 | HTTPS FTP |
-Validation report
Summary document | emd_32267_validation.pdf.gz | 388.4 KB | Display | EMDB validaton report |
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Full document | emd_32267_full_validation.pdf.gz | 387.9 KB | Display | |
Data in XML | emd_32267_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_32267_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32267 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32267 | HTTPS FTP |
-Related structure data
Related structure data | 7w2yMC 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 7vyfC 7vygC 7vyhC 7vyiC 7vynC 7vysC 7vz1C 7vz8C 7vzvC 7vzwC 7w00C 7w0hC 7w0rC 7w0yC 7w1oC 7w1pC 7w1tC 7w1uC 7w1vC 7w1zC 7w20C 7w2kC 7w2lC 7w2rC 7w2uC 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 (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_32267.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-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
+Macromolecule #7: Complex I subunit B13
+Macromolecule #8: Complex I-B14.5a
+Macromolecule #9: NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitoc...
+Macromolecule #10: Complex I-9kD
+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: Complex I-30kD
+Macromolecule #16: Complex I-49kD
+Macromolecule #17: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #20: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #21: Complex I-B16.6
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #25: Complex I-B17
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #31: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #32: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #33: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #34: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #35: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #36: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #40: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #41: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #44: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #45: IRON/SULFUR CLUSTER
+Macromolecule #46: FLAVIN MONONUCLEOTIDE
+Macromolecule #47: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
+Macromolecule #48: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #49: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,...
+Macromolecule #50: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
+Macromolecule #51: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #52: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #53: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
+Macromolecule #54: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #55: MAGNESIUM ION
+Macromolecule #56: CARDIOLIPIN
+Macromolecule #57: ZINC ION
+Macromolecule #58: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
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 |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 184754 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |