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Yorodumi- EMDB-13611: The acetogenin-bound complex I of Mus musculus resolved to 3.4 an... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13611 | |||||||||
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Title | The acetogenin-bound complex I of Mus musculus resolved to 3.4 angstroms | |||||||||
Map data | Globally sharpened map (postprocessed) in Relion | |||||||||
Sample |
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Function / homology | Function and homology information response to injury involved in regulation of muscle adaptation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / reproductive system development / Mitochondrial protein import / Respiratory electron transport / Glyoxylate metabolism and glycine degradation / RHOG GTPase cycle / respiratory system process / protein insertion into mitochondrial inner membrane ...response to injury involved in regulation of muscle adaptation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / reproductive system development / Mitochondrial protein import / Respiratory electron transport / Glyoxylate metabolism and glycine degradation / RHOG GTPase cycle / respiratory system process / protein insertion into mitochondrial inner membrane / response to light intensity / blastocyst hatching / circulatory system development / ubiquinone-6 biosynthetic process / cellular response to oxygen levels / psychomotor behavior / mitochondrial large ribosomal subunit binding / iron-sulfur cluster assembly complex / gliogenesis / neural precursor cell proliferation / mitochondrial respirasome / NADH dehydrogenase activity / cardiac muscle tissue development / [2Fe-2S] cluster assembly / oxygen sensor activity / respiratory chain complex I / cellular respiration / negative regulation of non-canonical NF-kappaB signal transduction / adult walking behavior / ubiquinone binding / cellular response to glucocorticoid stimulus / positive regulation of mitochondrial membrane potential / acyl binding / response to hydroperoxide / mitochondrial ribosome / electron transport coupled proton transport / mitochondrial ATP synthesis coupled electron transport / iron-sulfur cluster assembly / acyl carrier activity / mitochondrial translation / adult behavior / dopamine metabolic process / NADH:ubiquinone reductase (H+-translocating) / positive regulation of ATP biosynthetic process / mitochondrial respiratory chain complex I / proton motive force-driven mitochondrial ATP synthesis / apoptotic mitochondrial changes / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / neuron development / ATP synthesis coupled electron transport / cellular response to interferon-beta / negative regulation of intrinsic apoptotic signaling pathway / aerobic respiration / ATP metabolic process / cellular response to retinoic acid / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / response to cAMP / response to organonitrogen compound / tricarboxylic acid cycle / respiratory electron transport chain / ionotropic glutamate receptor binding / reactive oxygen species metabolic process / visual perception / Neutrophil degranulation / cerebellum development / neurogenesis / mitochondrion organization / response to hormone / fatty acid metabolic process / response to cocaine / regulation of mitochondrial membrane potential / response to nicotine / muscle contraction / synaptic membrane / kidney development / apoptotic signaling pathway / mitochondrial membrane / sensory perception of sound / regulation of protein phosphorylation / brain development / multicellular organism growth / response to hydrogen peroxide / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / negative regulation of cell growth / response to organic cyclic compound / cognition / circadian rhythm / positive regulation of protein catabolic process / NAD binding / positive regulation of fibroblast proliferation / FMN binding / myelin sheath / nervous system development / 4 iron, 4 sulfur cluster binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / house mouse (house mouse) / Mouse (mice) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Grba D / Hirst J | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: J Biol Chem / Year: 2022 Title: Cryo-electron microscopy reveals how acetogenins inhibit mitochondrial respiratory complex I. Authors: Daniel N Grba / James N Blaza / Hannah R Bridges / Ahmed-Noor A Agip / Zhan Yin / Masatoshi Murai / Hideto Miyoshi / Judy Hirst / Abstract: Mitochondrial complex I (NADH:ubiquinone oxidoreductase), a crucial enzyme in energy metabolism, captures the redox potential energy from NADH oxidation/ubiquinone reduction to create the proton ...Mitochondrial complex I (NADH:ubiquinone oxidoreductase), a crucial enzyme in energy metabolism, captures the redox potential energy from NADH oxidation/ubiquinone reduction to create the proton motive force used to drive ATP synthesis in oxidative phosphorylation. High-resolution single-particle electron cryo-EM analyses have provided detailed structural knowledge of the catalytic machinery of complex I, but not of the molecular principles of its energy transduction mechanism. Although ubiquinone is considered to bind in a long channel at the interface of the membrane-embedded and hydrophilic domains, with channel residues likely involved in coupling substrate reduction to proton translocation, no structures with the channel fully occupied have yet been described. Here, we report the structure (determined by cryo-EM) of mouse complex I with a tight-binding natural product acetogenin inhibitor, which resembles the native substrate, bound along the full length of the expected ubiquinone-binding channel. Our structure reveals the mode of acetogenin binding and the molecular basis for structure-activity relationships within the acetogenin family. It also shows that acetogenins are such potent inhibitors because they are highly hydrophobic molecules that contain two specific hydrophilic moieties spaced to lock into two hydrophilic regions of the otherwise hydrophobic channel. The central hydrophilic section of the channel does not favor binding of the isoprenoid chain when the native substrate is fully bound but stabilizes the ubiquinone/ubiquinol headgroup as it transits to/from the active site. Therefore, the amphipathic nature of the channel supports both tight binding of the amphipathic inhibitor and rapid exchange of the ubiquinone/ubiquinol substrate and product. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13611.map.gz | 324.2 MB | EMDB map data format | |
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Header (meta data) | emd-13611-v30.xml emd-13611.xml | 70.2 KB 70.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13611_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_13611.png | 122.1 KB | ||
Masks | emd_13611_msk_1.map | 347.6 MB | Mask map | |
Others | emd_13611_additional_1.map.gz emd_13611_additional_2.map.gz emd_13611_half_map_1.map.gz emd_13611_half_map_2.map.gz | 277.8 MB 274.8 MB 277.6 MB 277.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13611 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13611 | HTTPS FTP |
-Related structure data
Related structure data | 7psaMC 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 |
EM raw data | EMPIAR-10927 (Title: Single particle cryo-EM dataset of Mus musculus mitochondrial complex I bound with an acetogenin inhibitor Data size: 3.3 TB Data #1: Single-particle cryo-EM dataset of Mus musculus mitochondrial complex I co-purified with the inhibitor acetogenin [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13611.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Globally sharpened map (postprocessed) in Relion | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.043 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13611_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered consensus map from Relion
File | emd_13611_additional_1.map | ||||||||||||
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Annotation | Unfiltered consensus map from Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Locally sharpened map using LocalDeblur
File | emd_13611_additional_2.map | ||||||||||||
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Annotation | Locally sharpened map using LocalDeblur | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_13611_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_13611_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mitochondrial NADH:ubiquinone oxidoreductase from Mus musculus
+Supramolecule #1: Mitochondrial NADH:ubiquinone oxidoreductase from Mus musculus
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #7: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+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: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #20: Acyl carrier protein, mitochondrial
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #30: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #44: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #45: IRON/SULFUR CLUSTER
+Macromolecule #46: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #47: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #48: FLAVIN MONONUCLEOTIDE
+Macromolecule #49: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #50: (3~{S},5~{S})-5-methyl-3-[(13~{R})-13-oxidanyl-13-[(2~{R},5~{R})-...
+Macromolecule #51: CARDIOLIPIN
+Macromolecule #52: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #53: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #54: ZINC ION
+Macromolecule #55: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.55 Component:
Details: pH 7.55 at 25 degrees Celsius | ||||||||
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Grid | Model: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR Details: 20 mA glow discharge. Followed by a 2-day PEGylation with a PEG-thiol reagent. | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000 |
Specialist optics | Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1286 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |