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基本情報
登録情報 | データベース: PDB / ID: 1w0j | ||||||
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タイトル | Beryllium fluoride inhibited bovine F1-ATPase | ||||||
![]() | (ATP SYNTHASE ...) x 3 | ||||||
![]() | HYDROLASE / ATP PHOSPHORYLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP SYNTHASE / F1FO ATP SYNTHASE / F1-ATPASE / ATP SYNTHESIS / ATP-BINDING | ||||||
機能・相同性 | ![]() Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / Mitochondrial protein degradation / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase ...Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / Mitochondrial protein degradation / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Kagawa, R. / Montgomery, M.G. / Braig, K. / Walker, J.E. / Leslie, A.G.W. | ||||||
![]() | ![]() タイトル: The Structure of Bovine F1-ATPase Inhibited by Adp and Beryllium Fluoride 著者: Kagawa, R. / Montgomery, M.G. / Braig, K. / Leslie, A.G.W. / Walker, J.E. #1: ![]() タイトル: Structure of Bovine Mitochondrial F1-ATPase with Nucleotide Bound to All Three Catalytic Sites; Implications for the Mechanism of Rotary Catalysis 著者: Menz, R.I. / Walker, J.E. / Leslie, A.G.W. #2: ![]() タイトル: The Structure of the Central Stalk in Bovine F1-ATPase at 2.4A Resolution 著者: Gibbons, C. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. #3: ![]() タイトル: Molecular Architecture of the Rotary Motor in ATP Synthase 著者: Stock, D. / Leslie, A.G.W. / Walker, J.E. #4: ![]() タイトル: ATP Synthesis by Rotary Catalysis (Nobel Lecture) 著者: Walker, J.E. #5: ![]() タイトル: Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria 著者: Abrahams, J.P. / Leslie, A.G.W. / Lutter, R. / Walker, J.E. #6: ジャーナル: J.Mol.Biol. / 年: 1993 タイトル: Crystallization of F1-ATPase from Bovine Heart Mitochondria. 著者: Lutter, R. / Abrahams, J.P. / Van Raaij, M.J. / Todd, R.J. / Lundqvist, T. / Buchanan, S.K. / Leslie, A.G. / Walker, J.E. | ||||||
履歴 |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 609.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 495.9 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 2.1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2.1 MB | 表示 | |
XML形式データ | ![]() | 115.5 KB | 表示 | |
CIF形式データ | ![]() | 161.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
-ATP SYNTHASE ... , 3種, 7分子 ABCDEFG
#1: タンパク質 | 分子量: 55301.207 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #2: タンパク質 | 分子量: 51757.836 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #3: タンパク質 | | 分子量: 30185.674 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
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-非ポリマー , 6種, 1054分子 ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#4: 化合物 | ChemComp-ADP / #5: 化合物 | ChemComp-MG / #6: 化合物 | ChemComp-GOL / #7: 化合物 | #8: 化合物 | ChemComp-PO4 / | #9: 水 | ChemComp-HOH / | |
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-詳細
構成要素の詳細 | THE F1-ATPASE MOLECULE HAS THREE COPIES OF THE NON-CATALYTIC ALPHA SUBUNIT AND THREE COPIES OF THE ...THE F1-ATPASE MOLECULE HAS THREE COPIES OF THE NON-CATALYTIC ALPHA SUBUNIT AND THREE COPIES OF THE CATALYTIC BETA SUBUNIT. IN THE 1994 REFERENCE, THE BETA SUBUNITS WERE LABELED ACCORDING TO THE BOUND NUCLEOTIDE |
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配列の詳細 | REFERENCE: 1) FOR THE ALPHA SUBUNIT: J.E.WALKER,S.J.POWELL, O.VINAS AND M.J.RUNSWICK, BIOCHEMISTRY ...REFERENCE: 1) FOR THE ALPHA SUBUNIT: J.E.WALKER,S.J.POWELL, O.VINAS AND M.J.RUNSWICK, BIOCHEMIST |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.99 Å3/Da / 溶媒含有率: 54 % |
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結晶化 | pH: 8.2 詳細: CRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN THE STRUCTURE., pH 8.20 |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2002年3月15日 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.94 Å / 相対比: 1 |
反射 | 解像度: 2.2→45.2 Å / Num. obs: 185113 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / 冗長度: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.1 |
反射 シェル | 解像度: 2.2→2.32 Å / 冗長度: 1.4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.7 / % possible all: 51.1 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB CODE 1E1Q, NATIVE BOVINE MITOCHONDRIAL F1- ATPASE 解像度: 2.2→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / 交差検証法: THROUGHOUT / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: THE PHOSPHATE GROUP ADJACENT TO THE P-LOOP OF THE BETA(E) SUBUNIT (CHAIN E) IN THE COORDINATES HAS A HIGH B FACTOR AND DOES NOT HAVE THE EXPECTED HYDROGEN BONDS TO THE PROTEIN. IT IS POSSIBLE ...詳細: THE PHOSPHATE GROUP ADJACENT TO THE P-LOOP OF THE BETA(E) SUBUNIT (CHAIN E) IN THE COORDINATES HAS A HIGH B FACTOR AND DOES NOT HAVE THE EXPECTED HYDROGEN BONDS TO THE PROTEIN. IT IS POSSIBLE THAT THIS IS NOT, IN FACT, A PHOSPHATE, AND IT PROBABLY DOES NOT REPRESENT A PHYSIOLOGICALLY RELEVANT PHOSPHATE BINDING SITE.
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 48.59 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.2→20 Å
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拘束条件 |
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