+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11260 | |||||||||
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Title | Deactive complex I, open1 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity ...NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / : / membrane => GO:0016020 / ATP metabolic process / respiratory electron transport chain / reactive oxygen species metabolic process / FAD binding / regulation of mitochondrial membrane potential / electron transport chain / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / circadian rhythm / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / protein-containing complex binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) / Sheep (sheep) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Kampjut D / Sazanov LA | |||||||||
Funding support | European Union, 2 items
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Citation | Journal: Science / Year: 2020 Title: The coupling mechanism of mammalian respiratory complex I. Authors: Domen Kampjut / Leonid A Sazanov / Abstract: Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different ...Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11260.map.gz | 28.3 MB | EMDB map data format | |
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Header (meta data) | emd-11260-v30.xml emd-11260.xml | 56.7 KB 56.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11260_fsc.xml | 17.2 KB | Display | FSC data file |
Images | emd_11260.png | 84.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11260 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11260 | HTTPS FTP |
-Validation report
Summary document | emd_11260_validation.pdf.gz | 363.1 KB | Display | EMDB validaton report |
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Full document | emd_11260_full_validation.pdf.gz | 362.2 KB | Display | |
Data in XML | emd_11260_validation.xml.gz | 11.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11260 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11260 | HTTPS FTP |
-Related structure data
Related structure data | 6zksMC 6zk9C 6zkaC 6zkbC 6zkcC 6zkdC 6zkeC 6zkfC 6zkgC 6zkhC 6zkiC 6zkjC 6zkkC 6zklC 6zkmC 6zknC 6zkoC 6zkpC 6zkqC 6zkrC 6zktC 6zkuC 6zkvC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11260.map.gz / Format: CCP4 / Size: 30.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.055 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Deactive complex I, open1
+Supramolecule #1: Deactive complex I, open1
+Macromolecule #1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #2: Uncharacterized protein
+Macromolecule #3: NADH:ubiquinone oxidoreductase core subunit S1
+Macromolecule #4: Mitochondrial complex I, 49 kDa subunit
+Macromolecule #5: NADH:ubiquinone oxidoreductase core subunit S3
+Macromolecule #6: Mitochondrial complex I, PSST subunit
+Macromolecule #7: Mitochondrial complex I, TYKY subunit
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #9: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #14: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #15: Uncharacterized protein
+Macromolecule #16: NADH:ubiquinone oxidoreductase subunit B5
+Macromolecule #17: Acyl carrier protein
+Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #19: Mitochondrial complex I, PDSW subunit
+Macromolecule #20: Mitochondrial complex I, 10 kDa subunit
+Macromolecule #21: Mitochondrial complex I, 13 kDa subunit
+Macromolecule #22: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #23: NADH:ubiquinone oxidoreductase subunit A9
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #25: Uncharacterized protein
+Macromolecule #26: NADH:ubiquinone oxidoreductase subunit A6
+Macromolecule #27: Uncharacterized protein
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #30: NADH:ubiquinone oxidoreductase subunit S5
+Macromolecule #31: NADH:ubiquinone oxidoreductase subunit A3
+Macromolecule #32: NADH:ubiquinone oxidoreductase subunit B3
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #34: NADH:ubiquinone oxidoreductase subunit B4
+Macromolecule #35: Mitochondrial complex I, B16.6 subunit
+Macromolecule #36: Uncharacterized protein
+Macromolecule #37: NADH:ubiquinone oxidoreductase subunit B7
+Macromolecule #38: NADH:ubiquinone oxidoreductase subunit B9
+Macromolecule #39: NADH:ubiquinone oxidoreductase subunit B2
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #41: Uncharacterized protein
+Macromolecule #42: Mitochondrial complex I, KFYI subunit
+Macromolecule #43: Mitochondrial complex I, MNLL subunit
+Macromolecule #44: Mitochondrial complex I, MWFE subunit
+Macromolecule #45: IRON/SULFUR CLUSTER
+Macromolecule #46: FLAVIN MONONUCLEOTIDE
+Macromolecule #47: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #48: POTASSIUM ION
+Macromolecule #49: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #50: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
+Macromolecule #51: CARDIOLIPIN
+Macromolecule #52: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #53: ZINC ION
+Macromolecule #54: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #55: ADENOSINE MONOPHOSPHATE
+Macromolecule #56: MYRISTIC ACID
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |