+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5e8x | ||||||
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タイトル | TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D,I211V,Y249F,S280T, Y282F,S287N,A350C,L352F) IN COMPLEX WITH STAUROSPORINE | ||||||
要素 | TGF-beta receptor type-1 | ||||||
キーワード | TRANSFERASE/TRANSFERASE INHIBITOR / ALK5 / KINASE DOMAIN (キナーゼ) / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 extracellular structure organization / epicardium morphogenesis / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity ...extracellular structure organization / epicardium morphogenesis / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / positive regulation of mesenchymal stem cell proliferation / ventricular compact myocardium morphogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of vasculature development / regulation of epithelial to mesenchymal transition / activin receptor activity, type I / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor activity, type I / activin receptor complex / mesenchymal cell differentiation / neuron fate commitment / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / angiogenesis involved in coronary vascular morphogenesis / receptor protein serine/threonine kinase / germ cell migration / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / coronary artery morphogenesis / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / filopodium assembly / transforming growth factor beta binding / embryonic cranial skeleton morphogenesis / response to cholesterol / I-SMAD binding / collagen fibril organization / negative regulation of chondrocyte differentiation / endothelial cell activation / skeletal system morphogenesis / lens development in camera-type eye / endothelial cell proliferation / positive regulation of filopodium assembly / anterior/posterior pattern specification / artery morphogenesis / ventricular septum morphogenesis / roof of mouth development / SMAD binding / TGF-beta receptor signaling activates SMADs / negative regulation of endothelial cell proliferation / positive regulation of SMAD protein signal transduction / blastocyst development / regulation of protein ubiquitination / endothelial cell migration / bicellular tight junction / 上皮間葉転換 / positive regulation of epithelial to mesenchymal transition / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / Downregulation of TGF-beta receptor signaling / negative regulation of cell migration / transforming growth factor beta receptor signaling pathway / post-embryonic development / thymus development / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / skeletal system development / kidney development / positive regulation of apoptotic signaling pathway / 運動性 / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cellular response to growth factor stimulus / UCH proteinases / male gonad development / nervous system development / heart development / positive regulation of cell growth / 遺伝子発現の調節 / peptidyl-serine phosphorylation / in utero embryonic development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / Ub-specific processing proteases / regulation of cell cycle / エンドソーム / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / 脂質ラフト / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.45 Å | ||||||
データ登録者 | Sheriff, S. | ||||||
引用 | ジャーナル: Acta Crystallogr D Struct Biol / 年: 2016 タイトル: Crystal structures of apo and inhibitor-bound TGF beta R2 kinase domain: insights into TGF beta R isoform selectivity. 著者: Tebben, A.J. / Ruzanov, M. / Gao, M. / Xie, D. / Kiefer, S.E. / Yan, C. / Newitt, J.A. / Zhang, L. / Kim, K. / Lu, H. / Kopcho, L.M. / Sheriff, S. | ||||||
履歴 |
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-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 | 5e8x.cif.gz | 82 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5e8x.ent.gz | 57.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5e8x.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/e8/5e8x ftp://data.pdbj.org/pub/pdb/validation_reports/e8/5e8x | HTTPS FTP |
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-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: 35226.574 Da / 分子数: 1 / 断片: KINASE DOMAIN, UNP RESIDUES 200-503 / 変異: T204D,I211V,Y249F,S280T, Y282F,S287N,A350C,L352F / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TGFBR1, ALK5, SKR4 / プラスミド: PFASTBAC1 発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ) 参照: UniProt: P36897, receptor protein serine/threonine kinase |
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#2: 化合物 | ChemComp-STU / |
#3: 化合物 | ChemComp-GOL / |
#4: 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: 1.85 Å3/Da / 溶媒含有率: 33.54 % |
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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 / pH: 5.6 / 詳細: 23%(w/v) PEG3350, 3%(v/v) glcyerol |
-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: APS / ビームライン: 17-ID / 波長: 1 Å |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2015年4月16日 / 詳細: KIRKPATRICK-BAEZ |
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: 1.45→43.08 Å / Num. obs: 47034 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / 冗長度: 6.4 % / Biso Wilson estimate: 19.36 Å2 / Rsym value: 0.044 / Net I/σ(I): 19 |
反射 シェル | 解像度: 1.45→1.62 Å / 冗長度: 6.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 4.3 / Rejects: 0 / % possible all: 99.9 |
-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: 3TZM 解像度: 1.45→38.65 Å / Cor.coef. Fo:Fc: 0.9533 / Cor.coef. Fo:Fc free: 0.9473 / SU R Cruickshank DPI: 0.073 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.074 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.071
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原子変位パラメータ | Biso max: 84.61 Å2 / Biso mean: 25.82 Å2 / Biso min: 9.26 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 1.45→38.65 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.45→1.49 Å / Total num. of bins used: 20
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