+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16172 | |||||||||
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タイトル | Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete conformation 2 composition) | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 plastid outer membrane / anther dehiscence / TIM22 mitochondrial import inner membrane insertion complex / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / respiratory chain complex III / mitochondrial processing peptidase / plant-type cell wall / cold acclimation / P450-containing electron transport chain ...plastid outer membrane / anther dehiscence / TIM22 mitochondrial import inner membrane insertion complex / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / respiratory chain complex III / mitochondrial processing peptidase / plant-type cell wall / cold acclimation / P450-containing electron transport chain / 付加脱離酵素(リアーゼ); 炭素-酸素リアーゼ類; デヒドラターゼ類 / NADH dehydrogenase complex / protein insertion into mitochondrial inner membrane / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / : / quinol-cytochrome-c reductase / plant-type vacuole / vacuole / respiratory chain complex I / regulation of reactive oxygen species metabolic process / ubiquinol-cytochrome-c reductase activity / response to osmotic stress / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / porin activity / cobalt ion binding / pore complex / NADH:ubiquinone reductase (H+-translocating) / protein homotrimerization / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / ubiquinone binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / monoatomic ion transport / ATP synthesis coupled electron transport / response to salt stress / aerobic respiration / respiratory electron transport chain / chloroplast / mitochondrial membrane / electron transport chain / carbonate dehydratase activity / mitochondrial intermembrane space / transmembrane transport / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / FMN binding / peroxisome / 4 iron, 4 sulfur cluster binding / mitochondrial outer membrane / mitochondrial inner membrane / carbohydrate metabolic process / electron transfer activity / oxidoreductase activity / mitochondrial matrix / copper ion binding / heme binding / nucleolus / protein homodimerization activity / mitochondrion / proteolysis / zinc ion binding / extracellular region / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Arabidopsis thaliana (シロイヌナズナ) / thale cress (シロイヌナズナ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.8 Å | |||||||||
データ登録者 | Klusch N / Kuehlbrandt W | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Nat Plants / 年: 2023 タイトル: Cryo-EM structure of the respiratory I + III supercomplex from Arabidopsis thaliana at 2 Å resolution. 著者: Niklas Klusch / Maximilian Dreimann / Jennifer Senkler / Nils Rugen / Werner Kühlbrandt / Hans-Peter Braun / 要旨: Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis ...Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III with a co-purified ubiquinone in the Q site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane. | |||||||||
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_16172.map.gz | 99 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16172-v30.xml emd-16172.xml | 72.4 KB 72.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_16172_fsc.xml | 26.6 KB | 表示 | FSCデータファイル |
画像 | emd_16172.png | 186.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16172 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16172 | HTTPS FTP |
-関連構造データ
関連構造データ | 8bq6MC 8bedC 8beeC 8befC 8behC 8belC 8bepC 8bpxC 8bq5C C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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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_16172.map.gz / 形式: CCP4 / 大きさ: 1.6 GB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.573 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
-試料の構成要素
+全体 : Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Complete ...
+超分子 #1: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Complete ...
+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
+分子 #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
+分子 #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+分子 #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+分子 #7: NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
+分子 #8: NADH-ubiquinone oxidoreductase chain 1
+分子 #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial
+分子 #10: NADH-ubiquinone oxidoreductase chain 6
+分子 #11: NADH dehydrogenase subunit 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: AT3G07480.1
+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 1, mitochondrial
+分子 #21: Acyl carrier protein 2, mitochondrial
+分子 #22: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...
+分子 #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+分子 #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
+分子 #25: Outer envelope pore protein 16-3, chloroplastic/mitochondrial
+分子 #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
+分子 #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+分子 #28: At2g46540/F11C10.23
+分子 #29: Transmembrane protein
+分子 #30: Excitatory amino acid transporter
+分子 #31: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B
+分子 #32: At4g16450
+分子 #33: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
+分子 #34: P1
+分子 #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
+分子 #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A
+分子 #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+分子 #38: B15 -- 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-B
+分子 #42: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+分子 #43: Uncharacterized protein At1g67785
+分子 #44: Uncharacterized protein At2g27730, mitochondrial
+分子 #45: Gamma carbonic anhydrase-like 2, mitochondrial
+分子 #46: Gamma carbonic anhydrase 2, mitochondrial
+分子 #47: Gamma carbonic anhydrase 1, mitochondrial
+分子 #48: Probable mitochondrial-processing peptidase subunit alpha-1, mito...
+分子 #49: Probable mitochondrial-processing peptidase subunit beta, mitocho...
+分子 #50: Cytochrome b
+分子 #51: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
+分子 #52: Cytochrome c1 2, heme protein, mitochondrial
+分子 #53: Cytochrome b-c1 complex subunit 7-2, mitochondrial
+分子 #54: Cytochrome b-c1 complex subunit 8-1, mitochondrial
+分子 #55: Cytochrome b-c1 complex subunit 6-1, mitochondrial
+分子 #56: Cytochrome b-c1 complex subunit 9, mitochondrial
+分子 #57: Cytochrome b-c1 complex subunit 10, mitochondrial
+分子 #58: IRON/SULFUR CLUSTER
+分子 #59: FE2/S2 (INORGANIC) CLUSTER
+分子 #60: FLAVIN MONONUCLEOTIDE
+分子 #61: Ubiquinone-9
+分子 #62: FE (III) ION
+分子 #63: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #64: ZINC ION
+分子 #65: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+分子 #66: CROTONYL COENZYME A
+分子 #67: PROTOPORPHYRIN IX CONTAINING FE
+分子 #68: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14...
+分子 #69: UBIQUINONE-7
-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 | 0.18 mg/mL |
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緩衝液 | pH: 7.4 |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 400 / 支持フィルム - #0 - Film type ID: 1 / 支持フィルム - #0 - 材質: CARBON / 支持フィルム - #0 - トポロジー: CONTINUOUS / 支持フィルム - #1 - Film type ID: 2 / 支持フィルム - #1 - 材質: GRAPHENE / 支持フィルム - #1 - トポロジー: CONTINUOUS / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 15 sec. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 70 % / チャンバー内温度: 283.15 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 1.5 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 215000 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL |
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得られたモデル | PDB-8bq6: |