+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19147 | |||||||||
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Title | Closed Complex I from murine liver | |||||||||
Map data | composite map | |||||||||
Sample |
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Keywords | respiratory chain complex / mammalian mitochondria / MEMBRANE PROTEIN / ELECTRON TRANSPORT | |||||||||
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 electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / 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 / extrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / response to cAMP / tricarboxylic acid cycle / response to organonitrogen compound / respiratory electron transport chain / ionotropic glutamate receptor binding / reactive oxygen species metabolic process / visual perception / Neutrophil degranulation / neurogenesis / cerebellum development / 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) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Vercellino I / Sazanov LA | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: SCAF1 drives the compositional diversity of mammalian respirasomes. Authors: Irene Vercellino / Leonid A Sazanov / Abstract: Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies ...Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the 'canonical' respirasome (the C-respirasome, CICIIICIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the 'back' of CI, instead of the 'toe'. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions. #1: Journal: Acta Crystallogr., Sect. D: Biol. Cristallogr. / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Afonine PV / Adams PD | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19147.map.gz | 6.6 MB | EMDB map data format | |
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Header (meta data) | emd-19147-v30.xml emd-19147.xml | 67.2 KB 67.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19147_fsc.xml | 21.1 KB | Display | FSC data file |
Images | emd_19147.png | 52 KB | ||
Filedesc metadata | emd-19147.cif.gz | 14.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19147 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19147 | HTTPS FTP |
-Related structure data
Related structure data | 8rgrMC 8pw5C 8pw6C 8pw7C 8rgpC 8rgqC 8rgtC C: citing same article (ref.) M: atomic model generated by this map |
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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_19147.map.gz / Format: CCP4 / Size: 31.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | composite map | ||||||||||||||||||||
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
-Sample components
+Entire : Closed Complex I from murine liver
+Supramolecule #1: Closed Complex I from murine liver
+Macromolecule #1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #6: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #7: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #8: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #10: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #11: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #12: Acyl carrier protein, mitochondrial
+Macromolecule #13: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #14: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #17: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #18: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #19: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #20: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #21: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #22: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #23: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #24: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #33: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #44: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #45: IRON/SULFUR CLUSTER
+Macromolecule #46: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #47: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #48: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
+Macromolecule #49: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #50: FLAVIN MONONUCLEOTIDE
+Macromolecule #51: POTASSIUM ION
+Macromolecule #52: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #53: ZINC ION
+Macromolecule #54: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #55: CARDIOLIPIN
+Macromolecule #56: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #57: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.7 Component:
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Grid | Model: Quantifoil R0.6/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9453 / Average exposure time: 4.4 sec. / Average electron dose: 80.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |