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基本情報
登録情報 | データベース: EMDB / ID: EMD-30547 | |||||||||
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タイトル | Cryo-EM Structure of PSII at 1.95 angstrom resolution | |||||||||
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機能・相同性 | ![]() photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / extrinsic component of membrane / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / manganese ion binding / protein stabilization / electron transfer activity / iron ion binding / heme binding / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 1.95 Å | |||||||||
![]() | Kato K / Miyazaki N / Hamaguchi T / Nakajima Y / Akita F / Yonekura K / Shen JR | |||||||||
![]() | ![]() タイトル: High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams. 著者: Koji Kato / Naoyuki Miyazaki / Tasuku Hamaguchi / Yoshiki Nakajima / Fusamichi Akita / Koji Yonekura / Jian-Ren Shen / ![]() 要旨: Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are ...Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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 | ![]() | 21.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 39.1 KB 39.1 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.1 KB | 表示 | ![]() |
画像 | ![]() | 66.9 KB | ||
その他 | ![]() ![]() | 192 MB 192 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7d1tMC ![]() 7d1uC 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 ( |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data size: 427.6 Data #1: Unaligned multi-frame micrographs of PSII recorded by CRYO ARM 300 [micrographs - multiframe]) |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.822 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
-ハーフマップ: #1
ファイル | emd_30547_half_map_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: #2
ファイル | emd_30547_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : PSII dimer
+超分子 #1: PSII dimer
+分子 #1: Photosystem II protein D1
+分子 #2: Photosystem II CP47 reaction center protein
+分子 #3: Photosystem II CP43 reaction center protein
+分子 #4: Photosystem II D2 protein
+分子 #5: Cytochrome b559 subunit alpha
+分子 #6: Cytochrome b559 subunit beta
+分子 #7: Photosystem II reaction center protein H
+分子 #8: Photosystem II reaction center protein I
+分子 #9: Photosystem II reaction center protein J
+分子 #10: Photosystem II reaction center protein K
+分子 #11: Photosystem II reaction center protein L
+分子 #12: Photosystem II reaction center protein M
+分子 #13: Photosystem II manganese-stabilizing polypeptide
+分子 #14: Photosystem II reaction center protein T
+分子 #15: Photosystem II 12 kDa extrinsic protein
+分子 #16: Cytochrome c-550
+分子 #17: Photosystem II reaction center protein Ycf12
+分子 #18: Photosystem II reaction center protein X
+分子 #19: Photosystem II reaction center protein Z
+分子 #20: Photosystem II protein Y
+分子 #21: CA-MN4-O5 CLUSTER
+分子 #22: FE (II) ION
+分子 #23: CHLORIDE ION
+分子 #24: CHLOROPHYLL A
+分子 #25: PHEOPHYTIN A
+分子 #26: BETA-CAROTENE
+分子 #27: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+分子 #28: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+分子 #29: UNKNOWN LIGAND
+分子 #30: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+分子 #31: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+分子 #32: DODECYL-BETA-D-MALTOSIDE
+分子 #33: BICARBONATE ION
+分子 #34: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+分子 #35: PROTOPORPHYRIN IX CONTAINING FE
+分子 #36: MAGNESIUM ION
+分子 #37: HEME C
+分子 #38: (3R)-beta,beta-caroten-3-ol
+分子 #39: water
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 2.0 mg/mL | ||||||
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緩衝液 | pH: 6 / 構成要素:
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 200 / 支持フィルム - 材質: CARBON / 前処理 - タイプ: PLASMA CLEANING | ||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
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電子顕微鏡法
顕微鏡 | JEOL CRYO ARM 300 |
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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: COUNTING / 平均電子線量: 83.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |