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基本情報
登録情報 | データベース: EMDB / ID: EMD-13078 | |||||||||
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タイトル | Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana (digitonin-extracted) | |||||||||
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機能・相同性 | ![]() plastid thylakoid membrane / regulation of protein dephosphorylation / photoinhibition / photosystem II antenna complex / photosynthesis, light harvesting in photosystem II / nonphotochemical quenching / sequestering of metal ion / PSII associated light-harvesting complex II / chloroplast stromal thylakoid / thylakoid lumen ...plastid thylakoid membrane / regulation of protein dephosphorylation / photoinhibition / photosystem II antenna complex / photosynthesis, light harvesting in photosystem II / nonphotochemical quenching / sequestering of metal ion / PSII associated light-harvesting complex II / chloroplast stromal thylakoid / thylakoid lumen / response to high light intensity / thylakoid membrane / regulation of stomatal movement / chloroplast thylakoid / plastoglobule / chloroplast thylakoid lumen / vacuolar transport / photosystem II assembly / photosystem II oxygen evolving complex / response to abscisic acid / photosynthesis, light harvesting in photosystem I / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / : / apoplast / thylakoid / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / photosynthetic electron transport chain / poly(U) RNA binding / response to herbicide / photosystem II / plastid / chlorophyll binding / chloroplast stroma / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / response to light stimulus / photosynthetic electron transport in photosystem II / photosynthesis / chloroplast / membrane => GO:0016020 / electron transfer activity / protein stabilization / endosome / iron ion binding / protein domain specific binding / mRNA binding / heme binding / endoplasmic reticulum / nucleus / metal ion binding / plasma membrane / cytosol 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: 2.79 Å | |||||||||
![]() | Graca AT / Hall M / Persson K / Schroder WP | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction. 著者: André T Graça / Michael Hall / Karina Persson / Wolfgang P Schröder / ![]() 要旨: In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the ...In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated MnCaO-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation. #1: ![]() 年: 2018 タイトル: Real-space refinement in PHENIX for cryo-EM and crystallography 著者: Afonine PV / Poon BK / Read RJ / Sobolev OV / Terwilliger TC / Urzhumtsev A / Adams PD | |||||||||
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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文書・要旨 | ![]() | 266.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 265.9 KB | 表示 | |
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ボクセルのサイズ | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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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試料の構成要素
+全体 : Photosystem II - Light Harvesting Complex II supercomplex (PSII-L...
+超分子 #1: Photosystem II - Light Harvesting Complex II supercomplex (PSII-L...
+超分子 #2: CP24-LHCII (M-trimer)
+超分子 #3: LHCII S-trimer
+超分子 #4: CP29
+超分子 #5: CP26
+超分子 #6: Photosystem II core complex (dimer)
+分子 #1: Lhcb1.4
+分子 #2: Lhcb3.1
+分子 #3: Chlorophyll a-b binding protein, chloroplastic
+分子 #4: Photosystem II protein D1
+分子 #5: Photosystem II CP47 reaction center protein
+分子 #6: Photosystem II CP43 reaction center protein
+分子 #7: Photosystem II D2 protein
+分子 #8: Cytochrome b559 subunit alpha
+分子 #9: Cytochrome b559 subunit beta (PsbF)
+分子 #10: Photosystem II reaction center protein H
+分子 #11: Photosystem II reaction center protein I
+分子 #12: Photosystem II reaction center protein K
+分子 #13: Photosystem II reaction center protein L
+分子 #14: Photosystem II reaction center protein M
+分子 #15: Oxygen-evolving enhancer protein 1-1, chloroplastic
+分子 #16: Photosystem II reaction center protein T
+分子 #17: Photosystem II reaction center W protein, chloroplastic
+分子 #18: PsbX
+分子 #19: Photosystem II reaction center protein Z
+分子 #20: Chlorophyll a-b binding protein CP26, chloroplastic
+分子 #21: Chlorophyll a-b binding protein 1, chloroplastic
+分子 #22: Chlorophyll a-b binding protein CP29.1, chloroplastic
+分子 #23: PsbTn
+分子 #24: CHLOROPHYLL B
+分子 #25: CHLOROPHYLL A
+分子 #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+分子 #27: PHEOPHYTIN A
+分子 #28: BETA-CAROTENE
+分子 #29: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+分子 #30: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+分子 #31: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+分子 #32: Digitonin
+分子 #33: BICARBONATE ION
+分子 #34: FE (II) ION
+分子 #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+分子 #36: CALCIUM ION
+分子 #37: CHLORIDE ION
+分子 #38: PROTOPORPHYRIN IX CONTAINING FE
+分子 #39: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+分子 #40: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...
+分子 #41: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+分子 #42: 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 | 1 mg/mL |
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緩衝液 | pH: 7.5 / 構成要素 - 名称: HEPES-KOH / 詳細: 10mM HEPES-KOH pH7.5 + 0.01% (w/v) digitonin |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE / 詳細: 50 mA |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV / 詳細: Blot force -5 Wait time 1s Blotting time 5s. |
詳細 | Indicated sample concentration based on Chlorophyll measurement. |
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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: COUNTING / 撮影したグリッド数: 1 / 実像数: 12227 / 平均電子線量: 1.49 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: SPOT SCAN / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |