+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-32464 | ||||||||||||||||||
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タイトル | Subcomplexes B,M and L in the Cylic electron transfer supercomplex NDH-PSI from Arabidopsis | ||||||||||||||||||
マップデータ | |||||||||||||||||||
試料 |
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キーワード | Subcomplex B / subcomplex M / subcomplex L / Arabidopisis / plant / cyclic electron transport supercomplex / ELECTRON TRANSPORT | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 NAD(P)H dehydrogenase complex assembly / nitrite reductase complex [NAD(P)H] / NAD(P)H dehydrogenase complex (plastoquinone) / glucose-6-phosphate 1-epimerase activity / chloroplast stromal thylakoid / thylakoid lumen / chloroplast membrane / protein histidine kinase binding / P450-containing electron transport chain / chloroplast thylakoid ...NAD(P)H dehydrogenase complex assembly / nitrite reductase complex [NAD(P)H] / NAD(P)H dehydrogenase complex (plastoquinone) / glucose-6-phosphate 1-epimerase activity / chloroplast stromal thylakoid / thylakoid lumen / chloroplast membrane / protein histidine kinase binding / P450-containing electron transport chain / chloroplast thylakoid / トランスロカーゼ; ヒドロンの輸送の触媒; 酸化還元酵素反応を伴う / chloroplast thylakoid lumen / photosystem II oxygen evolving complex / thylakoid / NADPH dehydrogenase activity / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / plastid / extrinsic component of membrane / photosynthesis, light reaction / photosynthetic electron transport in photosystem I / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / chloroplast thylakoid membrane / ubiquinone binding / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / photosynthesis / ubiquinone biosynthetic process / chloroplast / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / protein folding / carbohydrate binding / response to oxidative stress / carbohydrate metabolic process / calcium ion binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Arabidopsis thaliana (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: 3.59 Å | ||||||||||||||||||
データ登録者 | Pan XW / Li M | ||||||||||||||||||
資金援助 | 中国, 5件
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引用 | ジャーナル: Mol Plant / 年: 2022 タイトル: Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana. 著者: Xiaodong Su / Duanfang Cao / Xiaowei Pan / Lifang Shi / Zhenfeng Liu / Luca Dall'Osto / Roberto Bassi / Xinzheng Zhang / Mei Li / 要旨: Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane- ...Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane-embedded NADH dehydrogenase-like (NDH) complex that contains at least 29 protein subunits and associates with photosystem I (PSI) to form the NDH-PSI supercomplex. Here, we report the 3.9 Å resolution structure of the Arabidopsis thaliana NDH-PSI (AtNDH-PSI) supercomplex. We constructed structural models for 26 AtNDH subunits, among which 11 are unique to chloroplasts and stabilize the core part of the NDH complex. In the supercomplex, one NDH can bind up to two PSI-light-harvesting complex I (PSI-LHCI) complexes at both sides of its membrane arm. Two minor LHCIs, Lhca5 and Lhca6, each present in one PSI-LHCI, interact with NDH and contribute to supercomplex formation and stabilization. Collectively, our study reveals the structural details of the AtNDH-PSI supercomplex assembly and provides a molecular basis for further investigation of the regulatory mechanism of CEF in plants. | ||||||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_32464.map.gz | 227.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-32464-v30.xml emd-32464.xml | 30.5 KB 30.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_32464.png | 73.7 KB | ||
Filedesc metadata | emd-32464.cif.gz | 9.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-32464 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32464 | HTTPS FTP |
-関連構造データ
-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_32464.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / 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: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : Cylic electron transfer supercomplex from Arabidopsis
+超分子 #1: Cylic electron transfer supercomplex from Arabidopsis
+分子 #1: NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic
+分子 #2: NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic
+分子 #3: NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic
+分子 #4: NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
+分子 #5: NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic
+分子 #6: NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic
+分子 #7: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic
+分子 #8: Photosynthetic NDH subunit of subcomplex B 1, chloroplastic
+分子 #9: Photosynthetic NDH subunit of subcomplex B 2, chloroplastic
+分子 #10: Photosynthetic NDH subunit of subcomplex B 3, chloroplastic
+分子 #11: NDH dependent flow 6
+分子 #12: Photosynthetic NDH subunit of subcomplex B 5, chloroplastic
+分子 #13: Photosynthetic NDH subunit of lumenal location 1, chloroplastic
+分子 #14: Photosynthetic NDH subunit of lumenal location 2, chloroplastic
+分子 #15: Photosynthetic NDH subunit of lumenal location 3, chloroplastic
+分子 #16: Photosynthetic NDH subunit of lumenal location 4, chloroplastic
+分子 #17: Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, ch...
+分子 #18: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+分子 #19: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+分子 #20: FE2/S2 (INORGANIC) CLUSTER
-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
緩衝液 | pH: 7.8 |
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凍結 | 凍結剤: ETHANE |
-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: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 60.0 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): 2.5 µm / 最小 デフォーカス(公称値): 1.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.59 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 136022 |
初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |