+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1opk | ||||||
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タイトル | Structural basis for the auto-inhibition of c-Abl tyrosine kinase | ||||||
要素 | Proto-oncogene tyrosine-protein kinase ABL1 | ||||||
キーワード | TRANSFERASE | ||||||
機能・相同性 | 機能・相同性情報 Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process / DN4 thymocyte differentiation ...Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process / DN4 thymocyte differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to epinephrine / regulation of cellular senescence / transitional one stage B cell differentiation / regulation of modification of synaptic structure / Regulation of actin dynamics for phagocytic cup formation / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / regulation of extracellular matrix organization / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / Myogenesis / bubble DNA binding / activated T cell proliferation / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / syntaxin binding / alpha-beta T cell differentiation / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / B cell proliferation / regulation of microtubule polymerization / cell leading edge / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / neuromuscular process controlling balance / platelet-derived growth factor receptor signaling pathway / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / endothelial cell migration / canonical NF-kappaB signal transduction / positive regulation of T cell migration / signal transduction in response to DNA damage / negative regulation of double-strand break repair via homologous recombination / BMP signaling pathway / negative regulation of endothelial cell apoptotic process / phagocytosis / positive regulation of substrate adhesion-dependent cell spreading / four-way junction DNA binding / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / ruffle / positive regulation of establishment of T cell polarity / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / ephrin receptor binding / actin filament polymerization / phosphotyrosine residue binding / response to endoplasmic reticulum stress / positive regulation of mitotic cell cycle / SH2 domain binding / substrate adhesion-dependent cell spreading / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / neural tube closure / establishment of localization in cell / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / neuron differentiation / epidermal growth factor receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / autophagy / cell-cell adhesion / cellular response to hydrogen peroxide / SH3 domain binding 類似検索 - 分子機能 | ||||||
生物種 | Mus musculus (ハツカネズミ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.8 Å | ||||||
データ登録者 | Nagar, B. / Hantschel, O. / Young, M.A. / Scheffzek, K. / Veach, D. / Bornmann, W. / Clarkson, B. / Superti-Furga, G. / Kuriyan, J. | ||||||
引用 | ジャーナル: Cell(Cambridge,Mass.) / 年: 2003 タイトル: Structural basis for the autoinhibition of c-Abl tyrosine kinase 著者: Nagar, B. / Hantschel, O. / Young, M.A. / Scheffzek, K. / Veach, D. / Bornmann, W. / Clarkson, B. / Superti-Furga, G. / Kuriyan, J. #1: ジャーナル: Cell(Cambridge,Mass.) / 年: 2003 タイトル: A myristoyl/phosphotyrosine switch regulates c-Abl 著者: Hantschel, O. / Nagar, B. / Guettler, S. / Kretzschmar, J. / Dorey, K. / Kuriyan, J. / Superti-Furga, G. | ||||||
履歴 |
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Remark 999 | SEQUENCE Numbering of the residues corresponds to the sequence database numbering of the isoform IV ...SEQUENCE Numbering of the residues corresponds to the sequence database numbering of the isoform IV of the protein. |
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1opk.cif.gz | 113.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1opk.ent.gz | 84.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1opk.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 1opk_validation.pdf.gz | 729.5 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1opk_full_validation.pdf.gz | 735.1 KB | 表示 | |
XML形式データ | 1opk_validation.xml.gz | 21.3 KB | 表示 | |
CIF形式データ | 1opk_validation.cif.gz | 31.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/op/1opk ftp://data.pdbj.org/pub/pdb/validation_reports/op/1opk | HTTPS FTP |
-関連構造データ
-リンク
-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: 56189.164 Da / 分子数: 1 / 断片: SH3-SH2-kinase domain / 変異: D382N / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: ABL1 / プラスミド: PFASTBAC 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P00520, EC: 2.7.1.112 |
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#2: 化合物 | ChemComp-MYR / |
#3: 化合物 | ChemComp-P16 / |
#4: 化合物 | ChemComp-GOL / |
#5: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.49 Å3/Da / 溶媒含有率: 50.22 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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: 7 詳細: 20% PEG 3350, 200 mM potassium nitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 20 ℃ / pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: シンクロトロン / サイト: ALS / ビームライン: 8.2.2 / 波長: 1.0781 Å |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2002年12月20日 / 詳細: mirrors |
放射 | モノクロメーター: Double crystal Si(111) / 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: 1.0781 Å / 相対比: 1 |
反射 | 解像度: 1.8→38 Å / Num. all: 50963 / Num. obs: 50963 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 7.1 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.057 / Net I/σ(I): 29.6 |
反射 シェル | 解像度: 1.8→1.86 Å / 冗長度: 6.7 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 5078 / Rsym value: 0.584 / % possible all: 100 |
反射 | *PLUS 最低解像度: 38 Å / Num. measured all: 560273 / Rmerge(I) obs: 0.057 |
反射 シェル | *PLUS 最高解像度: 1.8 Å / % possible obs: 100 % / Rmerge(I) obs: 0.584 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRIES 1M52, 2ABL 解像度: 1.8→37.59 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 35.0282 Å2 / ksol: 0.366818 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 30.9 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: 1.8→37.59 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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精密化 | *PLUS 最高解像度: 1.8 Å / 最低解像度: 38 Å | ||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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