+Open data
-Basic information
Entry | Database: PDB / ID: 8pw6 | ||||||
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Title | C respirasome from murine liver | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Respiratory chain super complex / mammalian mitochondria | ||||||
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 / adult behavior / hypothalamus development / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Vercellino, I. / Sazanov, L.A. | ||||||
Funding support | European Union, 1items
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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, P.V. / Adams, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pw6.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8pw6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8pw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/8pw6 ftp://data.pdbj.org/pub/pdb/validation_reports/pw/8pw6 | HTTPS FTP |
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-Related structure data
Related structure data | 17990MC 8pw5C 8pw7C 8rgpC 8rgqC 8rgrC 8rgtC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Cytochrome b-c1 complex subunit ... , 8 types, 17 molecules ALBMEPTFQGRHSJUKV
+Protein , 4 types, 7 molecules CNDO3T1U1
+Cytochrome c oxidase subunit ... , 13 types, 13 molecules nopqrstuvxyzw
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules 6C1D19Q17e1
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules 21s1
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 12 molecules P1S1V1W1q1r1O1X1Y1Z1a1b1
+NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules A1H1J1K1L1M1N1
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules c1d1
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules f1g1h1i1j1k1l1m1n1o1p1
+Non-polymers , 19 types, 94 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: C respirasome from murine liver / Type: COMPLEX / Entity ID: #1-#10, #24-#67, #11-#23 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 1.7 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) / Strain: CD1 / Organ: liver / Organelle: mitochondria | ||||||||||||||||||||
Buffer solution | pH: 7.7 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid type: Quantifoil R0.6/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4.4 sec. / Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9453 |
-Processing
EM software | Name: PHENIX / Version: 1.19_4092: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1758187 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103207 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Details: initial fitting done in chimera | ||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refine LS restraints |
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