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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: 2z0p | ||||||
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タイトル | Crystal structure of PH domain of Bruton's tyrosine kinase | ||||||
![]() | Tyrosine-protein kinase BTK | ||||||
![]() | SIGNALING PROTEIN / PH domain / PIP3C4 / ATP-binding / Disease mutation / Kinase / Membrane / Metal-binding / Nucleotide-binding / Nucleus / Phosphorylation / SH2 domain / SH3 domain / Transferase / Tyrosine-protein kinase / Zinc-finger / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
機能・相同性 | ![]() regulation of B cell cytokine production / monocyte proliferation / positive regulation of interleukin-17A production / eosinophil homeostasis / regulation of B cell apoptotic process / proteoglycan catabolic process / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell ...regulation of B cell cytokine production / monocyte proliferation / positive regulation of interleukin-17A production / eosinophil homeostasis / regulation of B cell apoptotic process / proteoglycan catabolic process / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell / neutrophil homeostasis / positive regulation of cGAS/STING signaling pathway / cellular response to molecule of fungal origin / positive regulation of type I hypersensitivity / MyD88 deficiency (TLR2/4) / cellular response to interleukin-7 / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / positive regulation of immunoglobulin production / phospholipase activator activity / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / positive regulation of NLRP3 inflammasome complex assembly / Fc-epsilon receptor signaling pathway / mesoderm development / B cell activation / phosphatidylinositol-3,4,5-trisphosphate binding / RHO GTPases Activate WASPs and WAVEs / phospholipase binding / cell maturation / positive regulation of phagocytosis / positive regulation of B cell proliferation / FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cellular response to reactive oxygen species / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / apoptotic signaling pathway / peptidyl-tyrosine phosphorylation / calcium-mediated signaling / positive regulation of NF-kappaB transcription factor activity / Regulation of actin dynamics for phagocytic cup formation / positive regulation of interleukin-6 production / G beta:gamma signalling through BTK / positive regulation of tumor necrosis factor production / DAP12 signaling / G alpha (12/13) signalling events / T cell receptor signaling pathway / ER-Phagosome pathway / cytoplasmic vesicle / protein tyrosine kinase activity / response to lipopolysaccharide / G alpha (q) signalling events / adaptive immune response / Potential therapeutics for SARS / intracellular signal transduction / protein phosphorylation / membrane raft / innate immune response / perinuclear region of cytoplasm / zinc ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Murayama, K. / Kato-Murayama, M. / Mishima, C. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() タイトル: Crystal structure of the Bruton's tyrosine kinase PH domain with phosphatidylinositol 著者: Murayama, K. / Kato-Murayama, M. / Mishima, C. / Akasaka, R. / Shirouzu, M. / Fukui, Y. / Yokoyama, S. | ||||||
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 | ![]() | 147.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 117.1 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 | ![]() | 1.8 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.8 MB | 表示 | |
XML形式データ | ![]() | 30 KB | 表示 | |
CIF形式データ | ![]() | 39 KB | 表示 | |
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 | ![]() 1btkS S: 精密化の開始モデル |
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類似構造データ | |
その他のデータベース |
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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
#1: タンパク質 | 分子量: 19983.014 Da / 分子数: 4 / 断片: PH domain / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q06187, non-specific protein-tyrosine kinase #2: 化合物 | ChemComp-ZN / #3: 化合物 | ChemComp-4PT / ( #4: 水 | ChemComp-HOH / | |
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-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: 2.71 Å3/Da / 溶媒含有率: 54.64 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: 25% PEG3350, 0.2M Li2SO4, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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 QUANTUM 210 / 検出器: CCD / 日付: 2006年12月2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: 1 Å / 相対比: 1 |
反射 | 解像度: 2.58→29.67 Å / Num. obs: 26621 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / 冗長度: 3.7 % / Biso Wilson estimate: 48.8 Å2 / Rsym value: 0.037 / Net I/σ(I): 24.9 |
反射 シェル | 解像度: 2.58→2.67 Å / Rsym value: 0.114 / % possible all: 99.7 |
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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 ENTRY 1BTK 解像度: 2.58→29.67 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1076225.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 46.8175 Å2 / ksol: 0.353675 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 52.4 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.58→29.67 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.58→2.74 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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