+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17989 | |||||||||
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Title | CS 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 / blastocyst hatching / circulatory system development / response to light intensity / pyramidal neuron development / response to mercury ion / mitochondrial respiratory chain complex III assembly / respiratory chain complex IV assembly / thalamus development / respiratory system process / protein insertion into mitochondrial inner membrane / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / psychomotor behavior / Mitochondrial protein degradation / cellular response to oxygen levels / iron-sulfur cluster assembly complex / : / mitochondrial large ribosomal subunit binding / regulation of oxidative phosphorylation / gliogenesis / : / response to alkaloid / neural precursor cell proliferation / cardiac muscle tissue development / cytochrome-c oxidase / : / [2Fe-2S] cluster assembly / oxidative phosphorylation / oxygen sensor activity / adult walking behavior / quinol-cytochrome-c reductase / respiratory chain complex I / cellular response to glucocorticoid stimulus / response to copper ion / deoxynucleoside kinase activity / response to glucagon / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of mitochondrial membrane potential / response to hydroperoxide / cellular respiration / ubiquinone-6 biosynthetic process / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / iron-sulfur cluster assembly / midbrain development / mitochondrial ribosome / hypothalamus development / adult behavior / mitochondrial electron transport, ubiquinol to cytochrome c / dopamine metabolic process / positive regulation of ATP biosynthetic process / mitochondrial translation / response to cobalamin / NADH:ubiquinone reductase (H+-translocating) / positive regulation of execution phase of apoptosis / apoptotic mitochondrial changes / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / neuron development / NADH dehydrogenase (ubiquinone) activity / response to hyperoxia / cellular response to interferon-beta / acyl carrier activity / quinone binding / animal organ regeneration / electron transport coupled proton transport / response to cadmium ion / ATP synthesis coupled electron transport / response to electrical stimulus / negative regulation of reactive oxygen species biosynthetic process / enzyme regulator activity / cellular response to retinoic acid / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway / ATP metabolic process / : / tricarboxylic acid cycle / visual perception / lactation / aerobic respiration Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 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_17989.map.gz | 12.7 MB | EMDB map data format | |
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Header (meta data) | emd-17989-v30.xml emd-17989.xml | 96.4 KB 96.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17989_fsc.xml | 21.2 KB | Display | FSC data file |
Images | emd_17989.png | 110 KB | ||
Filedesc metadata | emd-17989.cif.gz | 18.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17989 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17989 | HTTPS FTP |
-Validation report
Summary document | emd_17989_validation.pdf.gz | 544.3 KB | Display | EMDB validaton report |
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Full document | emd_17989_full_validation.pdf.gz | 543.9 KB | Display | |
Data in XML | emd_17989_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_17989_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17989 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17989 | HTTPS FTP |
-Related structure data
Related structure data | 8pw5MC 8pw6C 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_17989.map.gz / Format: CCP4 / Size: 55.2 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 : SC respirasome from murine liver
+Supramolecule #1: SC 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: Cox7a2l protein
+Macromolecule #12: Cytochrome c oxidase subunit 1
+Macromolecule #13: Cytochrome c oxidase subunit 2
+Macromolecule #14: Cytochrome c oxidase subunit 3
+Macromolecule #15: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
+Macromolecule #16: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #17: Cytochrome c oxidase subunit 5B, mitochondrial
+Macromolecule #18: Cytochrome c oxidase subunit 6A2, mitochondrial
+Macromolecule #19: Cytochrome c oxidase subunit 6B1
+Macromolecule #20: Cytochrome c oxidase subunit 6C
+Macromolecule #21: Cytochrome c oxidase subunit 7B, mitochondrial
+Macromolecule #22: Cytochrome c oxidase subunit 7C, mitochondrial
+Macromolecule #23: Cytochrome c oxidase subunit 8B, mitochondrial
+Macromolecule #24: Cytochrome c oxidase subunit 7A2, mitochondrial
+Macromolecule #25: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #26: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #27: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #28: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #29: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #30: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #31: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #33: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #34: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #36: Acyl carrier protein, mitochondrial
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #41: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #42: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #43: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #44: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #45: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #46: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #47: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #48: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #49: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #50: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #51: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #52: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #53: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #54: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #55: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #56: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #57: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #58: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #59: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #60: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #61: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #62: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #63: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #64: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #65: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #66: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #67: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #68: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #69: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #70: CARDIOLIPIN
+Macromolecule #71: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #72: HEME C
+Macromolecule #73: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #74: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #75: COPPER (II) ION
+Macromolecule #76: SODIUM ION
+Macromolecule #77: HEME-A
+Macromolecule #78: MAGNESIUM ION
+Macromolecule #79: DINUCLEAR COPPER ION
+Macromolecule #80: ZINC ION
+Macromolecule #81: TRISTEAROYLGLYCEROL
+Macromolecule #82: IRON/SULFUR CLUSTER
+Macromolecule #83: FLAVIN MONONUCLEOTIDE
+Macromolecule #84: POTASSIUM ION
+Macromolecule #85: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #86: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #87: 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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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 |