+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4kxz | ||||||
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タイトル | crystal structure of tgfb2 in complex with GC2008. | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / Cysteine knot (シスチンノット) / Fab / Various growth functions (TGF-beta) / TGF-beta antagonist (GC2008) / TGF-beta receptors | ||||||
機能・相同性 | 機能・相同性情報 regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / ascending aorta morphogenesis / uterine wall breakdown / cardioblast differentiation / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis ...regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / ascending aorta morphogenesis / uterine wall breakdown / cardioblast differentiation / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / regulation of transforming growth factor beta2 production / atrial septum morphogenesis / positive regulation of heart contraction / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / signaling / secondary palate development / positive regulation of stress-activated MAPK cascade / glial cell migration / somatic stem cell division / heart valve morphogenesis / atrial septum primum morphogenesis / endocardial cushion fusion / membranous septum morphogenesis / positive regulation of integrin biosynthetic process / cardiac epithelial to mesenchymal transition / neural retina development / eye development / cranial skeletal system development / embryonic digestive tract development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / outflow tract septum morphogenesis / negative regulation of Ras protein signal transduction / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / collagen fibril organization / embryonic limb morphogenesis / positive regulation of cell adhesion mediated by integrin / dopamine biosynthetic process / embryo development ending in birth or egg hatching / 歯の発生 / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / cardiac muscle cell proliferation / endocardial cushion morphogenesis / generation of neurons / hair follicle morphogenesis / ventricular septum morphogenesis / positive regulation of epithelial cell migration / positive regulation of Notch signaling pathway / activation of protein kinase activity / TGF-beta receptor signaling activates SMADs / inner ear development / uterus development / positive regulation of SMAD protein signal transduction / 造血 / positive regulation of cell division / hair follicle development / ECM proteoglycans / neuron development / 上皮間葉転換 / positive regulation of epithelial to mesenchymal transition / positive regulation of cell cycle / salivary gland morphogenesis / heart morphogenesis / extrinsic apoptotic signaling pathway / epithelial cell differentiation / negative regulation of angiogenesis / 好中球 / transforming growth factor beta receptor signaling pathway / platelet alpha granule lumen / response to progesterone / kidney development / skeletal system development / cytokine activity / neural tube closure / positive regulation of protein secretion / growth factor activity / wound healing / cell morphogenesis / negative regulation of cell growth / response to wounding / positive regulation of miRNA transcription / male gonad development / positive regulation of neuron apoptotic process / positive regulation of immune response / negative regulation of epithelial cell proliferation / 遊走 / Platelet degranulation / regulation of cell population proliferation / heart development / amyloid-beta binding / positive regulation of cell growth / collagen-containing extracellular matrix / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction 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: 2.83 Å | ||||||
データ登録者 | Mathieu, M. / Moulin, A.G. / Wei, R. | ||||||
引用 | ジャーナル: Protein Sci. / 年: 2014 タイトル: Structures of a pan-specific antagonist antibody complexed to different isoforms of TGF beta reveal structural plasticity of antibody-antigen interactions. 著者: Moulin, A. / Mathieu, M. / Lawrence, C. / Bigelow, R. / Levine, M. / Hamel, C. / Marquette, J.P. / Le Parc, J. / Loux, C. / Ferrari, P. / Capdevila, C. / Dumas, J. / Dumas, B. / Rak, A. / ...著者: Moulin, A. / Mathieu, M. / Lawrence, C. / Bigelow, R. / Levine, M. / Hamel, C. / Marquette, J.P. / Le Parc, J. / Loux, C. / Ferrari, P. / Capdevila, C. / Dumas, J. / Dumas, B. / Rak, A. / Bird, J. / Qiu, H. / Pan, C.Q. / Edmunds, T. / Wei, R.R. | ||||||
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 | 4kxz.cif.gz | 415.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4kxz.ent.gz | 352.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4kxz.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/kx/4kxz ftp://data.pdbj.org/pub/pdb/validation_reports/kx/4kxz | 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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単位格子 |
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-要素
-タンパク質 , 1種, 4分子 ABDE
#1: タンパク質 | 分子量: 12732.597 Da / 分子数: 4 / 断片: unp residues 303-414 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TGFB2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61812 |
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-抗体 , 2種, 8分子 HJNQILMP
#2: 抗体 | 分子量: 23907.832 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) #3: 抗体 | 分子量: 23425.934 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) |
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-非ポリマー , 3種, 232分子
#4: 化合物 | ChemComp-MES / #5: 化合物 | ChemComp-PE5 / | #6: 水 | ChemComp-HOH / | |
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-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: 3.17 Å3/Da / 溶媒含有率: 61.24 % |
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結晶化 | 温度: 296 K / 手法: 蒸気拡散法 / pH: 6 詳細: 35% PEG400, 100mM MES, VAPOR DIFFUSION, temperature 296K, pH 6.0 |
-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: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.98011 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2012年1月25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: 0.98011 Å / 相対比: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 2.83→48.73 Å / Num. all: 74556 / Num. obs: 74205 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 68.63 Å2 / Rmerge(I) obs: 0.121 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル |
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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: 分子置換 / 解像度: 2.83→48.73 Å / Cor.coef. Fo:Fc: 0.9354 / Cor.coef. Fo:Fc free: 0.9069 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.841 / 交差検証法: THROUGHOUT / σ(F): 0
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原子変位パラメータ | Biso max: 149.82 Å2 / Biso mean: 51.0971 Å2 / Biso min: 16.86 Å2
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Refine analyze | Luzzati coordinate error obs: 0.334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.83→48.73 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.83→2.9 Å / Total num. of bins used: 20
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