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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 5u1x | |||||||||
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タイトル | Crystal structure of the ATP-gated P2X7 ion channel bound to allosteric antagonist JNJ47965567 | |||||||||
![]() | P2X purinoceptor | |||||||||
![]() | MEMBRANE PROTEIN / membrane protein: ATP-gated ion channel: allosteric antagonist bound: closed state | |||||||||
機能・相同性 | ![]() NAD transport / phagolysosome assembly / phospholipid transfer to membrane / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / gamma-aminobutyric acid secretion / pore complex assembly / positive regulation of interleukin-1 alpha production / negative regulation of cell volume / plasma membrane organization ...NAD transport / phagolysosome assembly / phospholipid transfer to membrane / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / gamma-aminobutyric acid secretion / pore complex assembly / positive regulation of interleukin-1 alpha production / negative regulation of cell volume / plasma membrane organization / positive regulation of gamma-aminobutyric acid secretion / collagen metabolic process / : / response to fluid shear stress / positive regulation of prostaglandin secretion / T cell apoptotic process / bleb assembly / mitochondrial depolarization / ceramide biosynthetic process / vesicle budding from membrane / positive regulation of T cell apoptotic process / prostaglandin secretion / cellular response to dsRNA / glutamate secretion / positive regulation of glutamate secretion / negative regulation of bone resorption / skeletal system morphogenesis / positive regulation of macrophage cytokine production / phospholipid translocation / negative regulation of MAPK cascade / positive regulation of mitochondrial depolarization / response to ATP / response to zinc ion / T cell homeostasis / synaptic vesicle exocytosis / membrane protein ectodomain proteolysis / protein secretion / positive regulation of bone mineralization / T cell proliferation / response to electrical stimulus / response to mechanical stimulus / extrinsic apoptotic signaling pathway / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / sensory perception of pain / reactive oxygen species metabolic process / mitochondrion organization / positive regulation of interleukin-1 beta production / positive regulation of protein secretion / lipopolysaccharide binding / protein catabolic process / neuromuscular junction / cell morphogenesis / T cell mediated cytotoxicity / protein processing / response to calcium ion / positive regulation of T cell mediated cytotoxicity / positive regulation of interleukin-6 production / MAPK cascade / cell-cell junction / presynapse / postsynapse / response to lipopolysaccharide / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / response to xenobiotic stimulus / inflammatory response / positive regulation of protein phosphorylation / external side of plasma membrane / neuronal cell body / mitochondrion / ATP binding / identical protein binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Karasawa, A. / Kawate, T. | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural basis for subtype-specific inhibition of the P2X7 receptor. 著者: Karasawa, A. / Kawate, T. | |||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 81.5 KB | 表示 | ![]() |
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PDB形式 | ![]() | 57.7 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 976.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 982.4 KB | 表示 | |
XML形式データ | ![]() | 14.6 KB | 表示 | |
CIF形式データ | ![]() | 18.5 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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1 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 38716.234 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: Both the N- and C-termini are disordered and the electron density was not well-defined. 由来: (組換発現) ![]() ![]() 遺伝子: P2RX7 発現宿主: ![]() ![]() 参照: UniProt: G1M6C4 | ||
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#2: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
#3: 糖 | #4: 化合物 | ChemComp-7RV / | |
-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: 5.22 Å3/Da / 溶媒含有率: 76.42 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 詳細: 100 mM HEPES or Tris (pH 6.0-7.5), 100 mM NaCl, 4% ethylene glycol, 15% glycerol, 27-32% PEG-400 or 31-36% PEG-300, 0.1 mg/mL lipid mixture (60% POPE, 20% POPG, and 20% cholesterol), and 1 mM JNJ-47965567 PH範囲: 6.0-7.5 |
-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: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2015年7月10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: 0.9774 Å / 相対比: 1 | ||||||||||||||||||||||||||||||
反射 | 解像度: 3.1→48.88 Å / Num. obs: 14815 / % possible obs: 100 % / 冗長度: 10.1 % / Biso Wilson estimate: 107.11 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Net I/σ(I): 12.1 | ||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1 / Rejects: _
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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: A740003 bound P2X7 解像度: 3.201→48.88 Å / SU ML: 0.48 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.66
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 201.46 Å2 / Biso mean: 103.6362 Å2 / Biso min: 53.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 3.201→48.88 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %
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