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基本情報
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タイトル | Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by sucrose density | |||||||||||||||||||||
![]() | Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum | |||||||||||||||||||||
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![]() | PHOTOSYNTHESIS | |||||||||||||||||||||
機能・相同性 | ![]() organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / electron transfer activity / iron ion binding / heme binding ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding / plasma membrane 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: 2.24 Å | |||||||||||||||||||||
![]() | Tani K / Kanno R / Harada A / Kobayashi A / Minamino A / Nakamura N / Ji X-C / Purba ER / Hall M / Yu L-J ...Tani K / Kanno R / Harada A / Kobayashi A / Minamino A / Nakamura N / Ji X-C / Purba ER / Hall M / Yu L-J / Madigan MT / Mizoguchi A / Iwasaki K / Humbel BM / Kimura Y / Wang-Otomo Z-Y | |||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum. 著者: Kazutoshi Tani / Ryo Kanno / Ayaka Harada / Yuki Kobayashi / Akane Minamino / Shinji Takenaka / Natsuki Nakamura / Xuan-Cheng Ji / Endang R Purba / Malgorzata Hall / Long-Jiang Yu / Michael T ...著者: Kazutoshi Tani / Ryo Kanno / Ayaka Harada / Yuki Kobayashi / Akane Minamino / Shinji Takenaka / Natsuki Nakamura / Xuan-Cheng Ji / Endang R Purba / Malgorzata Hall / Long-Jiang Yu / Michael T Madigan / Akira Mizoguchi / Kenji Iwasaki / Bruno M Humbel / Yukihiro Kimura / Zheng-Yu Wang-Otomo / ![]() ![]() ![]() 要旨: The mesophilic purple sulfur phototrophic bacterium Allochromatium (Alc.) vinosum (bacterial family Chromatiaceae) has been a favored model for studies of bacterial photosynthesis and sulfur ...The mesophilic purple sulfur phototrophic bacterium Allochromatium (Alc.) vinosum (bacterial family Chromatiaceae) has been a favored model for studies of bacterial photosynthesis and sulfur metabolism, and its core light-harvesting (LH1) complex has been a focus of numerous studies of photosynthetic light reactions. However, despite intense efforts, no high-resolution structure and thorough biochemical analysis of the Alc. vinosum LH1 complex have been reported. Here we present cryo-EM structures of the Alc. vinosum LH1 complex associated with reaction center (RC) at 2.24 Å resolution. The overall structure of the Alc. vinosum LH1 resembles that of its moderately thermophilic relative Alc. tepidum in that it contains multiple pigment-binding α- and β-polypeptides. Unexpectedly, however, six Ca ions were identified in the Alc. vinosum LH1 bound to certain α1/β1- or α1/β3-polypeptides through a different Ca-binding motif from that seen in Alc. tepidum and other Chromatiaceae that contain Ca-bound LH1 complexes. Two water molecules were identified as additional Ca-coordinating ligands. Based on these results, we reexamined biochemical and spectroscopic properties of the Alc. vinosum LH1-RC. While modest but distinct effects of Ca were detected in the absorption spectrum of the Alc. vinosum LH1 complex, a marked decrease in thermostability of its LH1-RC complex was observed upon removal of Ca. The presence of Ca in the photocomplex of Alc. vinosum suggests that Ca-binding to LH1 complexes may be a common adaptation in species of Chromatiaceae for conferring spectral and thermal flexibility on this key component of their photosynthetic machinery. | |||||||||||||||||||||
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マップデータ | ![]() | 394.5 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 32.1 KB 32.1 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 16.4 KB | 表示 | ![]() |
画像 | ![]() | 99.8 KB | ||
Filedesc metadata | ![]() | 8.3 KB | ||
その他 | ![]() ![]() | 339 MB 338.9 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 | ![]() 8wduMC ![]() 8wdvC 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 | 類似検索 - 機能・相同性 ![]() |
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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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注釈 | Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.606 Å | ||||||||||||||||||||
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-ハーフマップ: Odd half map
ファイル | emd_37465_half_map_1.map | ||||||||||||
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注釈 | Odd half map | ||||||||||||
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密度ヒストグラム |
-ハーフマップ: Even half map
ファイル | emd_37465_half_map_2.map | ||||||||||||
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注釈 | Even half map | ||||||||||||
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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 : Photosynthetic LH1-RC complex from the purple sulfur phototrophic...
+超分子 #1: Photosynthetic LH1-RC complex from the purple sulfur phototrophic...
+分子 #1: Photosynthetic reaction center cytochrome c subunit
+分子 #2: Reaction center protein L chain
+分子 #3: Reaction center protein M chain
+分子 #4: Photosynthetic reaction center H subunit
+分子 #5: Antenna complex alpha/beta subunit
+分子 #6: Antenna complex alpha/beta subunit
+分子 #7: Antenna complex alpha/beta subunit
+分子 #8: Antenna complex alpha/beta subunit
+分子 #9: Antenna complex alpha/beta subunit
+分子 #10: PROTOPORPHYRIN IX CONTAINING FE
+分子 #11: MAGNESIUM ION
+分子 #12: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
+分子 #13: PALMITIC ACID
+分子 #14: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+分子 #15: BACTERIOCHLOROPHYLL A
+分子 #16: BACTERIOPHEOPHYTIN A
+分子 #17: Ubiquinone-8
+分子 #18: DODECYL-BETA-D-MALTOSIDE
+分子 #19: CARDIOLIPIN
+分子 #20: FE (III) ION
+分子 #21: MENAQUINONE 8
+分子 #22: SPIRILLOXANTHIN
+分子 #23: CALCIUM ION
+分子 #24: LAURYL DIMETHYLAMINE-N-OXIDE
+分子 #25: 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 | 4.0 mg/mL |
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緩衝液 | pH: 8 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 277 K / 装置: LEICA EM GP |
詳細 | This sample was monodisperse. |
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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 K3 (6k x 4k) / 検出モード: COUNTING / 平均露光時間: 2.0 sec. / 平均電子線量: 50.0 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 / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.2 µm 最小 デフォーカス(公称値): 0.7000000000000001 µm |
試料ステージ | 試料ホルダーモデル: JEOL / ホルダー冷却材: NITROGEN |
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画像解析
-原子モデル構築 1
初期モデル | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 温度因子: 44 / 当てはまり具合の基準: Correlation coefficient |
得られたモデル | ![]() PDB-8wdu: |