+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-35336 | |||||||||
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タイトル | Respiratory complex CI:CIII2, type IB, Wild type mouse under cold temperature | |||||||||
マップデータ | Cold Acclimated, Type IB of Respiratory Supercomplex CI:CIII2 | |||||||||
試料 |
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キーワード | Respiratory complex / Respiratory supercomplex / ELECTRON TRANSPORT | |||||||||
機能・相同性 | 機能・相同性情報 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 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.3 Å | |||||||||
データ登録者 | Shin Y-C / Liao M | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Cell / 年: 2024 タイトル: Structural basis of respiratory complex adaptation to cold temperatures. 著者: 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 / ...著者: 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 / 要旨: 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. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_35336.map.gz | 178.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-35336-v30.xml emd-35336.xml | 77.7 KB 77.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_35336_fsc.xml | 13.7 KB | 表示 | FSCデータファイル |
画像 | emd_35336.png | 189.6 KB | ||
マスクデータ | emd_35336_msk_1.map | 216 MB | マスクマップ | |
Filedesc metadata | emd-35336.cif.gz | 15.9 KB | ||
その他 | emd_35336_half_map_1.map.gz emd_35336_half_map_2.map.gz | 173.1 MB 173.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-35336 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35336 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_35336_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_35336_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_35336_validation.xml.gz | 20.9 KB | 表示 | |
CIF形式データ | emd_35336_validation.cif.gz | 27.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35336 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35336 | HTTPS FTP |
-関連構造データ
関連構造データ | 8ib9MC 8iaoC 8iapC 8iaqC 8iarC 8ib4C 8ib5C 8ib6C 8ib7C 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: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_35336.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Cold Acclimated, Type IB of Respiratory Supercomplex CI:CIII2 | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_35336_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Cold Acclimated, Type IB of Respiratory Supercomplex CI:CIII2
ファイル | emd_35336_half_map_1.map | ||||||||||||
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注釈 | Cold Acclimated, Type IB of Respiratory Supercomplex CI:CIII2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Cold Acclimated, Type IB of Respiratory Supercomplex CI:CIII2
ファイル | emd_35336_half_map_2.map | ||||||||||||
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注釈 | Cold Acclimated, Type IB of Respiratory Supercomplex CI:CIII2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Respiratory Supercomplex CI:CIII2
+超分子 #1: Respiratory Supercomplex CI:CIII2
+分子 #1: NADH-ubiquinone oxidoreductase chain 3
+分子 #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+分子 #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+分子 #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+分子 #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+分子 #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+分子 #7: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+分子 #8: NADH-ubiquinone oxidoreductase chain 1
+分子 #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+分子 #10: NADH-ubiquinone oxidoreductase chain 6
+分子 #11: NADH-ubiquinone oxidoreductase chain 4L
+分子 #12: NADH-ubiquinone oxidoreductase chain 5
+分子 #13: NADH-ubiquinone oxidoreductase chain 4
+分子 #14: NADH-ubiquinone oxidoreductase chain 2
+分子 #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+分子 #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+分子 #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+分子 #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+分子 #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+分子 #20: Acyl carrier protein, mitochondrial
+分子 #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+分子 #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+分子 #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+分子 #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+分子 #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+分子 #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+分子 #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+分子 #28: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+分子 #29: NADH dehydrogenase [ubiquinone] 1 subunit C2
+分子 #30: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+分子 #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+分子 #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+分子 #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+分子 #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+分子 #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+分子 #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+分子 #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+分子 #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+分子 #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+分子 #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+分子 #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+分子 #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+分子 #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+分子 #44: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+分子 #45: Cytochrome b-c1 complex subunit 1, mitochondrial
+分子 #46: Cytochrome b-c1 complex subunit 2, mitochondrial
+分子 #47: Cytochrome b
+分子 #48: Cytochrome c1, heme protein, mitochondrial
+分子 #49: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+分子 #50: Cytochrome b-c1 complex subunit 7
+分子 #51: Cytochrome b-c1 complex subunit 8
+分子 #52: Cytochrome b-c1 complex subunit 6, mitochondrial
+分子 #53: Cytochrome b-c1 complex subunit 9
+分子 #54: Cytochrome b-c1 complex subunit 10
+分子 #55: IRON/SULFUR CLUSTER
+分子 #56: UBIQUINONE-1
+分子 #57: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+分子 #58: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+分子 #59: FE2/S2 (INORGANIC) CLUSTER
+分子 #60: FLAVIN MONONUCLEOTIDE
+分子 #61: Ubiquinone-9
+分子 #62: CARDIOLIPIN
+分子 #63: ADENOSINE-5'-DIPHOSPHATE
+分子 #64: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #65: ZINC ION
+分子 #66: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
+分子 #67: PROTOPORPHYRIN IX CONTAINING FE
+分子 #68: UBIQUINONE-10
+分子 #69: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)...
+分子 #70: HEME C
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.33 mg/mL |
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緩衝液 | pH: 8 |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TALOS ARCTICA |
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撮影 | #0 - Image recording ID: 1 #0 - フィルム・検出器のモデル: GATAN K3 (6k x 4k) #0 - 平均電子線量: 46.1 e/Å2 / #1 - Image recording ID: 2 #1 - フィルム・検出器のモデル: GATAN K3 (6k x 4k) #1 - 平均電子線量: 45.9 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: OTHER / 撮影モード: OTHER / 最大 デフォーカス(公称値): 2.2 µm / 最小 デフォーカス(公称値): 1.0 µm |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |