+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19145 | |||||||||
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Title | Closed Complex I from murine brain | |||||||||
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 / response to light intensity ...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 / response to light intensity / protein insertion into mitochondrial inner membrane / blastocyst hatching / circulatory system development / psychomotor behavior / cellular response to oxygen levels / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / cardiac muscle tissue development / neural precursor cell proliferation / ubiquinone-6 biosynthetic process / mitochondrial respirasome / [2Fe-2S] cluster assembly / oxygen sensor activity / adult walking behavior / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to glucocorticoid stimulus / cellular respiration / positive regulation of mitochondrial membrane potential / response to hydroperoxide / iron-sulfur cluster assembly / mitochondrial ribosome / respiratory chain complex I / adult behavior / dopamine metabolic process / mitochondrial translation / NADH dehydrogenase activity / ubiquinone binding / NADH:ubiquinone reductase (H+-translocating) / positive regulation of ATP biosynthetic process / acyl binding / mitochondrial ATP synthesis coupled electron transport / proton motive force-driven mitochondrial ATP synthesis / electron transport coupled proton transport / mitochondrial respiratory chain complex I / apoptotic mitochondrial changes / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / neuron development / quinone binding / cellular response to interferon-beta / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / aerobic respiration / response to cAMP / tricarboxylic acid cycle / response to organonitrogen compound / ionotropic glutamate receptor binding / visual perception / respiratory electron transport chain / Neutrophil degranulation / reactive oxygen species metabolic process / mitochondrion organization / cerebellum development / neurogenesis / fatty acid metabolic process / electron transport chain / regulation of mitochondrial membrane potential / response to nicotine / response to cocaine / kidney development / synaptic membrane / response to hormone / muscle contraction / apoptotic signaling pathway / mitochondrial membrane / sensory perception of sound / regulation of protein phosphorylation / multicellular organism growth / brain development / response to hydrogen peroxide / mitochondrial intermembrane space / negative regulation of cell growth / response to organic cyclic compound / 2 iron, 2 sulfur cluster binding / 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: 3.0 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_19145.map.gz | 6.7 MB | EMDB map data format | |
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Header (meta data) | emd-19145-v30.xml emd-19145.xml | 67.2 KB 67.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19145_fsc.xml | 21.1 KB | Display | FSC data file |
Images | emd_19145.png | 100.4 KB | ||
Filedesc metadata | emd-19145.cif.gz | 14.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19145 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19145 | HTTPS FTP |
-Related structure data
Related structure data | 8rgpMC 8pw5C 8pw6C 8pw7C 8rgqC 8rgrC 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_19145.map.gz / Format: CCP4 / Size: 31.7 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 brain
+Supramolecule #1: Closed Complex I from murine brain
+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: 2.6 µm / Calibrated defocus min: 0.6 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: 10416 / Average exposure time: 4.4 sec. / Average electron dose: 80.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |