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Open data
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Basic information
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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 informationComplex IV assembly / response to D-galactosamine / Complex III assembly / TP53 Regulates Metabolic Genes / response to cobalamin / Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / mesenchymal stem cell proliferation / reproductive system development / blastocyst hatching ...Complex IV assembly / response to D-galactosamine / Complex III assembly / TP53 Regulates Metabolic Genes / response to cobalamin / Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / mesenchymal stem cell proliferation / reproductive system development / blastocyst hatching / sperm glycocalyx / perinuclear theca / psychomotor behavior / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Mitochondrial ribosome-associated quality control / Cytoprotection by HMOX1 / circulatory system development / Mitochondrial translation termination / Respiratory electron transport / respiratory chain complex IV assembly / response to mercury ion / mesenchymal stem cell differentiation / subthalamus development / pons development / protein insertion into mitochondrial inner membrane / response to light intensity / respiratory system process / cerebellar Purkinje cell layer development / : / mitochondrial respiratory chain complex III assembly / mitochondrial processing peptidase complex / sperm head-tail coupling apparatus / thalamus development / adult walking behavior / Mitochondrial protein degradation / pyramidal neuron development / respiratory chain complex IV / stem cell division / response to alkaloid / response to glucagon / mitochondrial large ribosomal subunit assembly / mitochondrial ATP synthesis coupled electron transport / protein lipoylation / cytochrome complex assembly / cellular response to oxygen levels / adult behavior / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / neural precursor cell proliferation / ubiquinone biosynthetic process / respiratory chain complex / gliogenesis / cytochrome-c oxidase / respiratory chain complex III / negative regulation of non-canonical NF-kappaB signal transduction / cellular respiration / response to hydroperoxide / cardiac muscle tissue development / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / oxidative phosphorylation / positive regulation of mitochondrial membrane potential / [2Fe-2S] cluster assembly / quinol-cytochrome-c reductase activity / oxygen sensor activity / sperm principal piece / cellular response to glucocorticoid stimulus / midbrain development / multicellular organism growth / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / iron-sulfur cluster assembly / response to copper ion / hypothalamus development / dopamine metabolic process / sperm end piece / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / animal organ regeneration / mitochondrial electron transport, NADH to ubiquinone / positive regulation of ATP biosynthetic process / proton motive force-driven mitochondrial ATP synthesis / electron transport coupled proton transport / acyl binding / regulation of protein phosphorylation / neuron development / mitochondrial respiratory chain complex I assembly / response to hyperoxia / response to electrical stimulus / response to cadmium ion / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / cerebellum development / reactive oxygen species metabolic process / respiratory chain complex I / positive regulation of execution phase of apoptosis / NADH dehydrogenase (ubiquinone) activity Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| 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: 2024Title: 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: 2018Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Afonine PV / Adams PD | |||||||||
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Structure visualization
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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 | 95.2 KB 95.2 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 | 18.8 KB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-17990 ftp://data.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 ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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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
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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 6A1, 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 8A, 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 |
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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 |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| 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 |
| 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 FIELD / 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 |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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FIELD EMISSION GUN



