+Open data
-Basic information
Entry | Database: PDB / ID: 8pw7 | |||||||||
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Title | A respirasome from murine liver | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Respiratory chain super complex / mammalian mitochondria | |||||||||
Function / homology | Function and homology information Complex IV assembly / Complex III assembly / subthalamus development / pons development / TP53 Regulates Metabolic Genes / response to injury involved in regulation of muscle adaptation / Protein lipoylation / reproductive system development / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis ...Complex IV assembly / Complex III assembly / subthalamus development / pons development / TP53 Regulates Metabolic Genes / response to injury involved in regulation of muscle adaptation / Protein lipoylation / reproductive system development / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / Mitochondrial protein import / cerebellar Purkinje cell layer development / RHOG GTPase cycle / respiratory chain complex III / Respiratory electron transport / protein insertion into mitochondrial inner membrane / circulatory system development / blastocyst hatching / respiratory chain complex IV assembly / pyramidal neuron development / response to mercury ion / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / mitochondrial respiratory chain complex III assembly / thalamus development / respiratory system process / respiratory chain complex IV / psychomotor behavior / Mitochondrial protein degradation / regulation of oxidative phosphorylation / response to light intensity / cellular response to oxygen levels / iron-sulfur cluster assembly complex / ubiquinone-6 biosynthetic process / mitochondrial large ribosomal subunit binding / : / gliogenesis / : / response to alkaloid / neural precursor cell proliferation / oxidative phosphorylation / cytochrome-c oxidase / cardiac muscle tissue development / : / negative regulation of non-canonical NF-kappaB signal transduction / [2Fe-2S] cluster assembly / quinol-cytochrome-c reductase / adult walking behavior / oxygen sensor activity / response to copper ion / response to glucagon / cellular response to glucocorticoid stimulus / ubiquinol-cytochrome-c reductase activity / response to hydroperoxide / positive regulation of mitochondrial membrane potential / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / respiratory chain complex I / iron-sulfur cluster assembly / mitochondrial ribosome / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / adult behavior / mitochondrial translation / positive regulation of ATP biosynthetic process / response to cobalamin / dopamine metabolic process / positive regulation of execution phase of apoptosis / NADH:ubiquinone reductase (H+-translocating) / : / ubiquinone binding / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / electron transport coupled proton transport / acyl binding / response to hyperoxia / cellular response to interferon-beta / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / neuron development / animal organ regeneration / quinone binding / response to cadmium ion / enzyme regulator activity / ATP synthesis coupled electron transport / response to electrical stimulus / cellular response to retinoic acid / negative regulation of intrinsic apoptotic signaling pathway / muscle contraction / negative regulation of reactive oxygen species biosynthetic process / ATP metabolic process / extrinsic apoptotic signaling pathway / tricarboxylic acid cycle Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 | 8pw7.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8pw7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8pw7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pw7_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 8pw7_full_validation.pdf.gz | 4.3 MB | Display | |
Data in XML | 8pw7_validation.xml.gz | 339.3 KB | Display | |
Data in CIF | 8pw7_validation.cif.gz | 521.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/8pw7 ftp://data.pdbj.org/pub/pdb/validation_reports/pw/8pw7 | HTTPS FTP |
-Related structure data
Related structure data | 17991MC 8pw5C 8pw6C 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 c oxidase subunit ... , 13 types, 13 molecules nopqrstuvxywz
+Cytochrome b-c1 complex subunit ... , 8 types, 17 molecules ALBMEPTFQGRHSJUKV
+Protein , 4 types, 7 molecules CNDO3T1U1
+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, 90 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: A respirasome from murine liver / Type: COMPLEX / Entity ID: #1-#67 / 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 material: COPPER / 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 FIELD / 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57506 / Algorithm: FOURIER SPACE / 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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