+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17990 | |||||||||
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Title | C respirasome from murine liver | |||||||||
Map data | composite map | |||||||||
Sample |
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Keywords | Respiratory chain super complex / mammalian mitochondria / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information subthalamus development / pons development / response to injury involved in regulation of muscle adaptation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / TP53 Regulates Metabolic Genes / reproductive system development / Mitochondrial protein import / Respiratory electron transport / Glyoxylate metabolism and glycine degradation ...subthalamus development / pons development / response to injury involved in regulation of muscle adaptation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / TP53 Regulates Metabolic Genes / reproductive system development / Mitochondrial protein import / Respiratory electron transport / Glyoxylate metabolism and glycine degradation / cerebellar Purkinje cell layer development / RHOG GTPase cycle / respiratory system process / protein insertion into mitochondrial inner membrane / response to light intensity / blastocyst hatching / circulatory system development / pyramidal neuron development / respiratory chain complex IV assembly / response to mercury ion / ubiquinone-6 biosynthetic process / mitochondrial respirasome assembly / thalamus development / Cytoprotection by HMOX1 / respiratory chain complex IV / cellular response to oxygen levels / mitochondrial respiratory chain complex III assembly / psychomotor behavior / mitochondrial large ribosomal subunit binding / iron-sulfur cluster assembly complex / regulation of oxidative phosphorylation / gliogenesis / mitochondrial respiratory chain complex III / neural precursor cell proliferation / mitochondrial respiratory chain complex IV / mitochondrial respirasome / NADH dehydrogenase activity / cardiac muscle tissue development / [2Fe-2S] cluster assembly / response to alkaloid / oxygen sensor activity / cytochrome-c oxidase / respiratory chain complex I / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / negative regulation of non-canonical NF-kappaB signal transduction / adult walking behavior / ubiquinone binding / oxidative phosphorylation / cellular response to glucocorticoid stimulus / positive regulation of mitochondrial membrane potential / response to copper ion / response to glucagon / acyl binding / response to hydroperoxide / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial ribosome / electron transport coupled proton transport / cytochrome-c oxidase activity / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, ubiquinol to cytochrome c / iron-sulfur cluster assembly / acyl carrier activity / mitochondrial translation / hypothalamus development / adult behavior / midbrain development / dopamine metabolic process / NADH:ubiquinone reductase (H+-translocating) / response to cobalamin / 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 / response to hyperoxia / cellular response to interferon-beta / animal organ regeneration / enzyme regulator activity / negative regulation of intrinsic apoptotic signaling pathway / response to cadmium ion / aerobic respiration / response to electrical stimulus / 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 Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 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. Crystallogr. / 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_17990.map.gz | 8.7 MB | EMDB map data format | |
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Header (meta data) | emd-17990-v30.xml emd-17990.xml | 95.1 KB 95.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17990_fsc.xml | 21.2 KB | Display | FSC data file |
Images | emd_17990.png | 76.9 KB | ||
Filedesc metadata | emd-17990.cif.gz | 18.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17990 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17990 | HTTPS FTP |
-Related structure data
Related structure data | 8pw6MC 8pw5C 8pw7C 8rgpC 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_17990.map.gz / Format: CCP4 / Size: 54.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | composite map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
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 : C respirasome from murine liver
+Supramolecule #1: C respirasome from murine liver
+Macromolecule #1: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #2: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #3: Cytochrome b
+Macromolecule #4: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #5: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #6: Cytochrome b-c1 complex subunit 7
+Macromolecule #7: Cytochrome b-c1 complex subunit 8
+Macromolecule #8: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #9: Cytochrome b-c1 complex subunit 9
+Macromolecule #10: Cytochrome b-c1 complex subunit 10
+Macromolecule #11: Cytochrome c oxidase subunit 1
+Macromolecule #12: Cytochrome c oxidase subunit 2
+Macromolecule #13: Cytochrome c oxidase subunit 3
+Macromolecule #14: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
+Macromolecule #15: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #16: Cytochrome c oxidase subunit 5B, mitochondrial
+Macromolecule #17: Cytochrome c oxidase subunit 6A2, mitochondrial
+Macromolecule #18: Cytochrome c oxidase subunit 6B1
+Macromolecule #19: Cytochrome c oxidase subunit 6C
+Macromolecule #20: Cytochrome c oxidase subunit 7B, mitochondrial
+Macromolecule #21: Cytochrome c oxidase subunit 7C, mitochondrial
+Macromolecule #22: Cytochrome c oxidase subunit 8B, mitochondrial
+Macromolecule #23: Cytochrome c oxidase subunit 7A2, mitochondrial
+Macromolecule #24: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #25: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #26: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #27: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #28: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #29: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #30: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #32: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #33: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #35: Acyl carrier protein, mitochondrial
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #40: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #41: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #42: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #43: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #44: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #45: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #46: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #47: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #48: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #49: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #50: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #51: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #52: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #53: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #54: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #55: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #56: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #57: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #58: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #59: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #60: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #61: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #62: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #63: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #64: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #65: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #66: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #67: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #68: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #69: CARDIOLIPIN
+Macromolecule #70: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #71: HEME C
+Macromolecule #72: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #73: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #74: COPPER (II) ION
+Macromolecule #75: SODIUM ION
+Macromolecule #76: HEME-A
+Macromolecule #77: MAGNESIUM ION
+Macromolecule #78: DINUCLEAR COPPER ION
+Macromolecule #79: ZINC ION
+Macromolecule #80: TRISTEAROYLGLYCEROL
+Macromolecule #81: IRON/SULFUR CLUSTER
+Macromolecule #82: FLAVIN MONONUCLEOTIDE
+Macromolecule #83: POTASSIUM ION
+Macromolecule #84: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #85: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #86: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
-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 |