+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | A respirasome from murine liver | |||||||||
![]() | composite map, used to build the model | |||||||||
![]() |
| |||||||||
![]() | Respiratory chain super complex / mammalian mitochondria / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() Complex IV assembly / response to D-galactosamine / Complex III assembly / TP53 Regulates Metabolic Genes / 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 ...Complex IV assembly / response to D-galactosamine / Complex III assembly / TP53 Regulates Metabolic Genes / 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 / response to mercury ion / respiratory chain complex IV assembly / subthalamus development / pons development / Cytoprotection by HMOX1 / Respiratory electron transport / protein insertion into mitochondrial inner membrane / cerebellar Purkinje cell layer development / aerobic electron transport chain / blastocyst hatching / mitochondrial respiratory chain complex III assembly / response to alkaloid / pyramidal neuron development / respiratory system process / cellular respiration / psychomotor behavior / respiratory chain complex IV / thalamus development / Mitochondrial protein degradation / mesenchymal stem cell proliferation / cellular response to oxygen levels / response to light intensity / respiratory chain complex / reproductive system development / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / response to copper ion / response to glucagon / mesenchymal stem cell differentiation / circulatory system development / cytochrome-c oxidase / respiratory chain complex III / negative regulation of non-canonical NF-kappaB signal transduction / oxidative phosphorylation / cardiac muscle tissue development / quinol-cytochrome-c reductase / neural precursor cell proliferation / positive regulation of mitochondrial membrane potential / mitochondrial electron transport, cytochrome c to oxygen / [2Fe-2S] cluster assembly / oxygen sensor activity / adult walking behavior / response to hydroperoxide / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / stem cell division / cellular response to glucocorticoid stimulus / mitochondrial electron transport, ubiquinol to cytochrome c / iron-sulfur cluster assembly / response to cobalamin / hypothalamus development / mitochondrial ATP synthesis coupled electron transport / midbrain development / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / dopamine metabolic process / adult behavior / positive regulation of ATP biosynthetic process / NADH dehydrogenase activity / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / positive regulation of execution phase of apoptosis / response to electrical stimulus / respiratory chain complex I / animal organ regeneration / response to hyperoxia / NADH dehydrogenase (ubiquinone) activity / neuron development / quinone binding / response to cadmium ion / cellular response to interferon-beta / ATP synthesis coupled electron transport / response to hormone / lactation / extrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / tricarboxylic acid cycle / cellular response to retinoic acid / neurogenesis / Neutrophil degranulation / visual perception / response to nutrient / muscle contraction / reactive oxygen species metabolic process / aerobic respiration / cerebellum development / central nervous system development Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Vercellino I / Sazanov LA | |||||||||
Funding support | European Union, 1 items
| |||||||||
![]() | ![]() 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: ![]() Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Afonine PV / Adams PD | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 11.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 92.9 KB 92.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21.2 KB | Display | ![]() |
Images | ![]() | 42.5 KB | ||
Filedesc metadata | ![]() | 18.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 563 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 562.6 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | 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 |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-
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 |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.7 Component:
| ||||||||||||
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 |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: ![]() |
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 |