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Yorodumi- PDB-8ib7: Respiratory complex CIII2, focus-refined of type IA, Wild type mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ib7 | |||||||||
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Title | Respiratory complex CIII2, focus-refined of type IA, Wild type mouse under cold temperature | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / Respiratory complex / Respiratory supercomplex | |||||||||
Function / homology | Function and homology information Complex III assembly / subthalamus development / pons development / pyramidal neuron development / cerebellar Purkinje cell layer development / Respiratory electron transport / response to mercury ion / mitochondrial respiratory chain complex III assembly / thalamus development / respiratory chain complex III ...Complex III assembly / subthalamus development / pons development / pyramidal neuron development / cerebellar Purkinje cell layer development / Respiratory electron transport / response to mercury ion / mitochondrial respiratory chain complex III assembly / thalamus development / respiratory chain complex III / Mitochondrial protein degradation / : / : / response to alkaloid / quinol-cytochrome-c reductase / response to copper ion / ubiquinol-cytochrome-c reductase activity / response to glucagon / cellular respiration / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / response to cobalamin / electron transport coupled proton transport / response to hyperoxia / animal organ regeneration / response to cadmium ion / response to hormone / respiratory electron transport chain / hippocampus development / response to activity / mitochondrial membrane / metalloendopeptidase activity / response to toxic substance / 2 iron, 2 sulfur cluster binding / response to calcium ion / myelin sheath / response to ethanol / mitochondrial inner membrane / response to hypoxia / oxidoreductase activity / response to xenobiotic stimulus / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / protein-containing complex / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Shin, Y.-C. / Liao, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell / Year: 2024 Title: Structural basis of respiratory complex adaptation to cold temperatures. Authors: Young-Cheul Shin / Pedro Latorre-Muro / Amina Djurabekova / Oleksii Zdorevskyi / Christopher F Bennett / Nils Burger / Kangkang Song / Chen Xu / Joao A Paulo / Steven P Gygi / Vivek Sharma / ...Authors: Young-Cheul Shin / Pedro Latorre-Muro / Amina Djurabekova / Oleksii Zdorevskyi / Christopher F Bennett / Nils Burger / Kangkang Song / Chen Xu / Joao A Paulo / Steven P Gygi / Vivek Sharma / Maofu Liao / Pere Puigserver / Abstract: In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain. Yet, the structural basis of respiratory complex adaptation upon cold ...In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain. Yet, the structural basis of respiratory complex adaptation upon cold exposure remains elusive. Herein, we combined thermoregulatory physiology and cryoelectron microscopy (cryo-EM) to study endogenous respiratory supercomplexes from mice exposed to different temperatures. A cold-induced conformation of CI:III (termed type 2) supercomplex was identified with a ∼25° rotation of CIII around its inter-dimer axis, shortening inter-complex Q exchange space, and exhibiting catalytic states that favor electron transfer. Large-scale supercomplex simulations in mitochondrial membranes reveal how lipid-protein arrangements stabilize type 2 complexes to enhance catalytic activity. Together, our cryo-EM studies, multiscale simulations, and biochemical analyses unveil the thermoregulatory mechanisms and dynamics of increased respiratory capacity in brown fat at the structural and energetic level. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ib7.cif.gz | 809.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ib7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ib7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ib7_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 8ib7_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 8ib7_validation.xml.gz | 118 KB | Display | |
Data in CIF | 8ib7_validation.cif.gz | 177 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/8ib7 ftp://data.pdbj.org/pub/pdb/validation_reports/ib/8ib7 | HTTPS FTP |
-Related structure data
Related structure data | 35334MC 8iaoC 8iapC 8iaqC 8iarC 8ib4C 8ib5C 8ib6C 8ib9C 8ibaC 8ibbC 8ibcC 8ibdC 8ibeC 8ibfC 8ibgC 8ic4C 8ic5C 8xnlC 8xnmC 8xnnC 8xnoC 8xnpC 8xnqC 8xnrC 8xnsC 8xntC 8xnuC 8xnvC 8xnwC 8xnxC 8xnyC 8xnzC 8xo0C 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 AAAaABAbAEAIAeAFAfAGAgAHAhAJAjAKAk
#1: Protein | Mass: 52910.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZ13 #2: Protein | Mass: 48289.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DB77 #5: Protein | Mass: 29406.635 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR68, quinol-cytochrome-c reductase #6: Protein | Mass: 13587.532 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQB4 #7: Protein | Mass: 9783.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ69 #8: Protein | Mass: 10452.694 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P99028 #9: Protein | Mass: 7457.526 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8R1I1 #10: Protein | Mass: 6546.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPX8 |
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-Protein , 2 types, 4 molecules ACAcADAd
#3: Protein | Mass: 43240.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P00158 #4: Protein | Mass: 35374.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0M3, quinol-cytochrome-c reductase |
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-Non-polymers , 7 types, 21 molecules
#11: Chemical | ChemComp-HEM / #12: Chemical | ChemComp-3PE / #13: Chemical | #14: Chemical | #15: Chemical | ChemComp-CDL / #16: Chemical | #17: Chemical | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-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: Respiratory Supercomplex CI:CIII2 / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL |
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Molecular weight | Value: 1.32 MDa / Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.33 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company | ||||||||||||
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Microscopy | Model: FEI TALOS ARCTICA | ||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER | ||||||||||||
Electron lens | Mode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm | ||||||||||||
Image recording |
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-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151188 / Symmetry type: POINT |