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基本情報
登録情報 | データベース: PDB / ID: 4j9g | ||||||
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タイトル | Crystal structure of the ABL-SH3 domain complexed with the designed high-affinity peptide ligand P7 at pH7 | ||||||
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![]() | Transferase/unknown function / beta shandwich / SH3 domain / kinase / poly proline rich motifs / transferase / Transferase-unknown function complex | ||||||
機能・相同性 | ![]() : / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process ...: / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / transitional one stage B cell differentiation / regulation of postsynaptic specialization assembly / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / cerebellum morphogenesis / neuroepithelial cell differentiation / B cell proliferation involved in immune response / positive regulation of Wnt signaling pathway, planar cell polarity pathway / positive regulation of extracellular matrix organization / microspike assembly / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / mitochondrial depolarization / regulation of cell motility / positive regulation of establishment of T cell polarity / activated T cell proliferation / cellular response to dopamine / positive regulation of blood vessel branching / proline-rich region binding / negative regulation of mitotic cell cycle / regulation of Cdc42 protein signal transduction / mitogen-activated protein kinase binding / syntaxin binding / regulation of hematopoietic stem cell differentiation / alpha-beta T cell differentiation / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of dendrite development / peptidyl-tyrosine autophosphorylation / regulation of axon extension / regulation of T cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of cell-cell adhesion / HDR through Single Strand Annealing (SSA) / neuromuscular process controlling balance / positive regulation of osteoblast proliferation / Myogenesis / positive regulation of vasoconstriction / platelet-derived growth factor receptor-beta signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / Bergmann glial cell differentiation / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / regulation of microtubule polymerization / myoblast proliferation / associative learning / negative regulation of long-term synaptic potentiation / negative regulation of cellular senescence / actin monomer binding / signal transduction in response to DNA damage / negative regulation of BMP signaling pathway / positive regulation of focal adhesion assembly / RHO GTPases Activate WASPs and WAVEs / canonical NF-kappaB signal transduction / cardiac muscle cell proliferation / BMP signaling pathway / ephrin receptor signaling pathway / positive regulation of T cell migration / endothelial cell migration / negative regulation of double-strand break repair via homologous recombination / negative regulation of endothelial cell apoptotic process / cellular response to transforming growth factor beta stimulus / mismatch repair / regulation of cell adhesion / four-way junction DNA binding / spleen development / ephrin receptor binding / positive regulation of stress fiber assembly / ruffle / ERK1 and ERK2 cascade / actin filament polymerization / phosphotyrosine residue binding / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of interleukin-2 production / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / SH2 domain binding / positive regulation of mitotic cell cycle / protein kinase C binding / response to endoplasmic reticulum stress / positive regulation of release of sequestered calcium ion into cytosol / peptidyl-tyrosine phosphorylation / thymus development / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / integrin-mediated signaling pathway / post-embryonic development 類似検索 - 分子機能 | ||||||
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手法 | ![]() ![]() ![]() | ||||||
![]() | Camara-Artigas, A. | ||||||
![]() | ![]() タイトル: Crystal structure of the ABL-SH3 domain complexed with the designed high-affinity peptide ligand P7 著者: Camara-Artigas, A. #1: ![]() タイトル: Crystallization by capillary counter-diffusion and structure determination of the N114A mutant of the SH3 domain of Abl tyrosine kinase complexed with a high-affinity peptide ligand. 著者: Camara-Artigas, A. / Palencia, A. / Martinez, J.C. / Luque, I. / Gavira, J.A. / Garcia-Ruiz, J.M. #2: ![]() タイトル: Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl. 著者: Palencia, A. / Camara-Artigas, A. / Pisabarro, M.T. / Martinez, J.C. / Luque, I. | ||||||
履歴 |
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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 | ![]() | 86.5 KB | 表示 | ![]() |
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PDB形式 | ![]() | 66.9 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 480.1 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 481.1 KB | 表示 | |
XML形式データ | ![]() | 10.8 KB | 表示 | |
CIF形式データ | ![]() | 14.7 KB | 表示 | |
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-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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Components on special symmetry positions |
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要素
#1: タンパク質 | 分子量: 7009.694 Da / 分子数: 3 / 断片: SH3 domain (unp residues 60-121) / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: P00519, non-specific protein-tyrosine kinase #2: タンパク質・ペプチド | 分子量: 1059.212 Da / 分子数: 3 / 由来タイプ: 合成 #3: 化合物 | ChemComp-SO4 / | #4: 化合物 | ChemComp-GOL / | #5: 水 | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.01 Å3/Da / 溶媒含有率: 38.78 % |
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 詳細: 2M ammonium sulphate, 50 mM Litium Formiate, 10% glicerol, and 0.1 M MOPS , pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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 PILATUS 6M / 検出器: PIXEL / 日付: 2012年7月13日 詳細: vertical focusing mirror (VFM) and a horizontal focusing mirror (HFM), manufactured by IRELEC. | |||||||||||||||||||||
放射 | モノクロメーター: Si(111) channel-cut crystal monochromator and a pair of KB mirrors 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: 0.97951 Å / 相対比: 1 | |||||||||||||||||||||
Reflection | 冗長度: 6.2 % / 数: 111250 / Rmerge(I) obs: 0.069 / D res high: 1.8 Å / D res low: 74.746 Å / Num. obs: 17945 / % possible obs: 98.1 | |||||||||||||||||||||
Diffraction reflection shell |
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反射 | 解像度: 1.8→74.746 Å / Num. all: 18311 / Num. obs: 17945 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 6.2 % / Biso Wilson estimate: 20.634 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 14.2 | |||||||||||||||||||||
反射 シェル | Diffraction-ID: 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: 2O88 解像度: 1.8→38.701 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.2 / σ(F): 0 / σ(I): 0 / 位相誤差: 29.63 / 立体化学のターゲット値: ML
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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 / 溶媒モデル: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 105.2 Å2 / Biso mean: 36.5653 Å2 / Biso min: 11.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.8→38.701 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: 12
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