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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | A respirasome from murine liver | |||||||||
Map data | composite map, used to build the model | |||||||||
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 / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis ...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 / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Mitochondrial ribosome-associated quality control / response to mercury ion / Cytoprotection by HMOX1 / Mitochondrial translation termination / Respiratory electron transport / respiratory chain complex IV assembly / subthalamus development / pons development / protein insertion into mitochondrial inner membrane / cerebellar Purkinje cell layer development / mitochondrial respiratory chain complex III assembly / blastocyst hatching / respiratory system process / psychomotor behavior / pyramidal neuron development / Mitochondrial protein degradation / thalamus development / respiratory chain complex IV / response to light intensity / protein lipoylation / response to alkaloid / mesenchymal stem cell proliferation / cellular response to oxygen levels / iron-sulfur cluster assembly complex / reproductive system development / ubiquinone biosynthetic process / mitochondrial large ribosomal subunit binding / mitochondrial [2Fe-2S] assembly complex / gliogenesis / respiratory chain complex / cytochrome-c oxidase / mesenchymal stem cell differentiation / circulatory system development / negative regulation of non-canonical NF-kappaB signal transduction / respiratory chain complex III / cellular respiration / oxidative phosphorylation / response to glucagon / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / response to hydroperoxide / adult walking behavior / cardiac muscle tissue development / positive regulation of mitochondrial membrane potential / neural precursor cell proliferation / oxygen sensor activity / [2Fe-2S] cluster assembly / quinol-cytochrome-c reductase activity / cellular response to glucocorticoid stimulus / cytochrome-c oxidase activity / stem cell division / iron-sulfur cluster assembly / mitochondrial electron transport, ubiquinol to cytochrome c / response to copper ion / hypothalamus development / midbrain development / NADH:ubiquinone reductase (H+-translocating) / dopamine metabolic process / ubiquinone binding / adult behavior / positive regulation of ATP biosynthetic process / mitochondrial ATP synthesis coupled electron transport / electron transport coupled proton transport / proton motive force-driven mitochondrial ATP synthesis / mitochondrial electron transport, NADH to ubiquinone / acyl binding / mitochondrial respiratory chain complex I assembly / response to electrical stimulus / NADH dehydrogenase activity / oxidoreductase activity, acting on NAD(P)H / animal organ regeneration / respiratory chain complex I / positive regulation of execution phase of apoptosis / response to hyperoxia / NADH dehydrogenase (ubiquinone) activity / response to cadmium ion / acyl carrier activity / response to cAMP / neuron development / quinone binding / ATP synthesis coupled electron transport / enzyme regulator activity / cellular response to interferon-beta / tricarboxylic acid cycle / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / lactation / Neutrophil degranulation Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.5 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_17991.map.gz | 11.3 MB | EMDB map data format | |
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| Header (meta data) | emd-17991-v30.xml emd-17991.xml | 92.9 KB 92.9 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_17991_fsc.xml | 21.2 KB | Display | FSC data file |
| Images | emd_17991.png | 42.5 KB | ||
| Filedesc metadata | emd-17991.cif.gz | 18.8 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17991 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17991 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8pw7MC ![]() 8pw5C ![]() 8pw6C ![]() 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_17991.map.gz / Format: CCP4 / Size: 50.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | composite map, used to build the model | ||||||||||||||||||||||||||||||||||||
| 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 : A respirasome from murine liver
+Supramolecule #1: A respirasome from murine liver
+Macromolecule #1: Cytochrome c oxidase subunit 1
+Macromolecule #2: Cytochrome c oxidase subunit 2
+Macromolecule #3: Cytochrome c oxidase subunit 3
+Macromolecule #4: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
+Macromolecule #5: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #6: Cytochrome c oxidase subunit 5B, mitochondrial
+Macromolecule #7: Cytochrome c oxidase subunit 6A1, mitochondrial
+Macromolecule #8: Cytochrome c oxidase subunit 6B1
+Macromolecule #9: Cytochrome c oxidase subunit 6C
+Macromolecule #10: Cytochrome c oxidase subunit 7B, mitochondrial
+Macromolecule #11: Cytochrome c oxidase subunit 7C, mitochondrial
+Macromolecule #12: Cytochrome c oxidase subunit 7A2, mitochondrial
+Macromolecule #13: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #14: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #15: Cytochrome b
+Macromolecule #16: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #17: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #18: Cytochrome b-c1 complex subunit 7
+Macromolecule #19: Cytochrome b-c1 complex subunit 8
+Macromolecule #20: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #21: Cytochrome b-c1 complex subunit 9
+Macromolecule #22: Cytochrome b-c1 complex subunit 10
+Macromolecule #23: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #24: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #25: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #26: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #27: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #28: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #29: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #31: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #32: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #34: Acyl carrier protein, mitochondrial
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #39: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #40: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #41: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #42: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #43: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #44: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #45: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #46: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #47: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #48: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #49: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #50: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #51: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #52: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #53: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #54: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #55: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #56: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #57: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #58: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #59: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #60: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #61: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #62: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #63: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #64: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #65: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #66: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #67: Cytochrome c oxidase subunit 8A, mitochondrial
+Macromolecule #68: COPPER (II) ION
+Macromolecule #69: SODIUM ION
+Macromolecule #70: HEME-A
+Macromolecule #71: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #72: MAGNESIUM ION
+Macromolecule #73: DINUCLEAR COPPER ION
+Macromolecule #74: ZINC ION
+Macromolecule #75: TRISTEAROYLGLYCEROL
+Macromolecule #76: CARDIOLIPIN
+Macromolecule #77: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #78: HEME C
+Macromolecule #79: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #80: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+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 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. | ||||||||||||
| 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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Processing
FIELD EMISSION GUN



