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Yorodumi- EMDB-35313: Respiratory complex CI:CIII2, type I, Wild type mouse under therm... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35313 | |||||||||
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Title | Respiratory complex CI:CIII2, type I, Wild type mouse under thermoneutral temperature | |||||||||
Map data | Thermoneutral, Type I of Respiratory Supercomplex CI:CIII2 | |||||||||
Sample |
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Keywords | Respiratory complex / Respiratory supercomplex / ELECTRON TRANSPORT | |||||||||
Function / homology | Function and homology information Complex III assembly / subthalamus development / pons development / pyramidal neuron development / Mitochondrial protein import / cerebellar Purkinje cell layer development / response to injury involved in regulation of muscle adaptation / reproductive system development / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation ...Complex III assembly / subthalamus development / pons development / pyramidal neuron development / Mitochondrial protein import / cerebellar Purkinje cell layer development / response to injury involved in regulation of muscle adaptation / reproductive system development / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / response to mercury ion / protein insertion into mitochondrial inner membrane / mitochondrial respiratory chain complex III assembly / thalamus development / blastocyst hatching / circulatory system development / respiratory chain complex III / respiratory system process / psychomotor behavior / ubiquinone-6 biosynthetic process / Mitochondrial protein degradation / response to light intensity / cellular response to oxygen levels / : / iron-sulfur cluster assembly complex / : / : / mitochondrial large ribosomal subunit binding / response to alkaloid / gliogenesis / negative regulation of non-canonical NF-kappaB signal transduction / quinol-cytochrome-c reductase / response to copper ion / cellular response to glucocorticoid stimulus / neural precursor cell proliferation / cardiac muscle tissue development / ubiquinol-cytochrome-c reductase activity / response to glucagon / [2Fe-2S] cluster assembly / oxygen sensor activity / adult walking behavior / positive regulation of mitochondrial membrane potential / cellular respiration / midbrain development / response to hydroperoxide / : / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / ubiquinone binding / iron-sulfur cluster assembly / positive regulation of ATP biosynthetic process / adult behavior / response to cobalamin / dopamine metabolic process / NADH:ubiquinone reductase (H+-translocating) / positive regulation of execution phase of apoptosis / proton motive force-driven mitochondrial ATP synthesis / apoptotic mitochondrial changes / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / respiratory chain complex I / : / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / neuron development / acyl binding / response to hyperoxia / animal organ regeneration / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / cellular response to interferon-beta / negative regulation of intrinsic apoptotic signaling pathway / ATP synthesis coupled electron transport / quinone binding / response to cadmium ion / cellular response to retinoic acid / negative regulation of reactive oxygen species biosynthetic process / muscle contraction / extrinsic apoptotic signaling pathway / ionotropic glutamate receptor binding / tricarboxylic acid cycle / Neutrophil degranulation / aerobic respiration / visual perception / response to hormone / neurogenesis / respiratory electron transport chain / cerebellum development / reactive oxygen species metabolic process / kidney development / regulation of mitochondrial membrane potential / response to cocaine / hippocampus development / response to activity / synaptic membrane / mitochondrion organization Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Shin Y-C / Liao M | |||||||||
Funding support | United States, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35313.map.gz | 195 MB | EMDB map data format | |
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Header (meta data) | emd-35313-v30.xml emd-35313.xml | 77.5 KB 77.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35313_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_35313.png | 180.1 KB | ||
Masks | emd_35313_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-35313.cif.gz | 16 KB | ||
Others | emd_35313_half_map_1.map.gz emd_35313_half_map_2.map.gz | 187 MB 186.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35313 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35313 | HTTPS FTP |
-Validation report
Summary document | emd_35313_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_35313_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_35313_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | emd_35313_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35313 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35313 | HTTPS FTP |
-Related structure data
Related structure data | 8iaoMC 8iapC 8iaqC 8iarC 8ib4C 8ib5C 8ib6C 8ib7C 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: atomic model generated by this map C: citing same article (ref.) |
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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_35313.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Thermoneutral, Type I of Respiratory Supercomplex CI:CIII2 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_35313_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Thermoneutral, Type I of Respiratory Supercomplex CI:CIII2, half 2
File | emd_35313_half_map_1.map | ||||||||||||
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Annotation | Thermoneutral, Type I of Respiratory Supercomplex CI:CIII2, half 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Thermoneutral, Type I of Respiratory Supercomplex CI:CIII2, half 1
File | emd_35313_half_map_2.map | ||||||||||||
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Annotation | Thermoneutral, Type I of Respiratory Supercomplex CI:CIII2, half 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Respiratory Supercomplex CI:CIII2
+Supramolecule #1: Respiratory Supercomplex CI:CIII2
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #7: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #14: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #20: Acyl carrier protein, mitochondrial
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #30: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #44: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #45: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #46: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #47: Cytochrome b
+Macromolecule #48: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #49: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #50: Cytochrome b-c1 complex subunit 7
+Macromolecule #51: Cytochrome b-c1 complex subunit 8
+Macromolecule #52: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #53: Cytochrome b-c1 complex subunit 9
+Macromolecule #54: Cytochrome b-c1 complex subunit 10
+Macromolecule #55: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #56: CARDIOLIPIN
+Macromolecule #57: IRON/SULFUR CLUSTER
+Macromolecule #58: UBIQUINONE-1
+Macromolecule #59: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #60: FLAVIN MONONUCLEOTIDE
+Macromolecule #61: Ubiquinone-9
+Macromolecule #62: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #63: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #64: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #65: ZINC ION
+Macromolecule #66: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
+Macromolecule #67: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #68: UBIQUINONE-10
+Macromolecule #69: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)...
+Macromolecule #70: HEME C
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.33 mg/mL |
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Buffer | pH: 8 |
Grid | Material: GRAPHENE OXIDE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 46.6 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |