+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1u7f | ||||||
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タイトル | Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeric complex | ||||||
要素 |
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キーワード | SIGNALING PROTEIN / Smad / TGF-beta (TGF-β) / signal transduction (シグナル伝達) / protein complex (タンパク質複合体) / phosphorylation (リン酸化) | ||||||
機能・相同性 | 機能・相同性情報 nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / positive regulation of transforming growth factor beta3 production / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / transdifferentiation ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / positive regulation of transforming growth factor beta3 production / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / transdifferentiation / somite rostral/caudal axis specification / atrioventricular valve formation / sterol response element binding / paraxial mesoderm morphogenesis / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / positive regulation of luteinizing hormone secretion / regulation of hair follicle development / regulation of striated muscle tissue development / sebaceous gland development / SMAD protein complex / formation of anatomical boundary / epithelial cell migration / RUNX2 regulates bone development / immune system development / positive regulation of follicle-stimulating hormone secretion / co-SMAD binding / heteromeric SMAD protein complex / regulation of transforming growth factor beta2 production / neuron fate specification / filamin binding / epithelial to mesenchymal transition involved in endocardial cushion formation / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / DEAD/H-box RNA helicase binding / response to transforming growth factor beta / secondary palate development / bHLH transcription factor binding / pericardium development / FOXO-mediated transcription of cell cycle genes / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of chondrocyte differentiation / negative regulation of osteoblast proliferation / negative regulation of cardiac muscle hypertrophy / brainstem development / left ventricular cardiac muscle tissue morphogenesis / Transcriptional regulation of pluripotent stem cells / regulation of transforming growth factor beta receptor signaling pathway / embryonic foregut morphogenesis / atrioventricular canal development / negative regulation of wound healing / lens fiber cell differentiation / cardiac conduction system development / nuclear glucocorticoid receptor binding / positive regulation of extracellular matrix assembly / transforming growth factor beta receptor binding / primary miRNA processing / Germ layer formation at gastrulation / endoderm development / sulfate binding / Signaling by BMP / signal transduction involved in regulation of gene expression / Formation of definitive endoderm / cellular response to BMP stimulus / embryonic pattern specification / activin receptor signaling pathway / outflow tract septum morphogenesis / Signaling by Activin / cell-cell junction organization / Formation of axial mesoderm / SMAD protein signal transduction / Signaling by NODAL / regulation of epithelial cell proliferation / embryonic cranial skeleton morphogenesis / cardiac muscle hypertrophy in response to stress / gastrulation with mouth forming second / I-SMAD binding / Interleukin-37 signaling / neural crest cell differentiation / response to angiotensin / endothelial cell activation / Cardiogenesis / positive regulation of positive chemotaxis / osteoblast development / NOTCH4 Intracellular Domain Regulates Transcription / negative regulation of cardiac muscle hypertrophy in response to stress / RUNX3 regulates CDKN1A transcription / nuclear inner membrane / ureteric bud development / negative regulation of fat cell differentiation / branching involved in ureteric bud morphogenesis / DNA-binding transcription repressor activity / embryonic digit morphogenesis / adrenal gland development / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway 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: 2.6 Å | ||||||
データ登録者 | Chacko, B.M. / Qin, B.Y. / Tiwari, A. / Shi, G. / Lam, S. / Hayward, L.J. / de Caestecker, M. / Lin, K. | ||||||
引用 | ジャーナル: Mol.Cell / 年: 2004 タイトル: Structural basis of heteromeric smad protein assembly in tgf-Beta signaling 著者: Chacko, B.M. / Qin, B.Y. / Tiwari, A. / Shi, G. / Lam, S. / Hayward, L.J. / De Caestecker, M. / Lin, K. | ||||||
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 | 1u7f.cif.gz | 137.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1u7f.ent.gz | 107 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1u7f.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/u7/1u7f ftp://data.pdbj.org/pub/pdb/validation_reports/u7/1u7f | 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: 22467.271 Da / 分子数: 2 / 断片: MH2 and Linker domains / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SMAD3, MADH3 / プラスミド: pTXB1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): ER2566 / 参照: UniProt: P84022 #2: タンパク質 | | 分子量: 26060.693 Da / 分子数: 1 / 断片: MH2 and Linker domains / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SMAD4, MADH4, DPC4 / プラスミド: pGEX-4T2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): HB101 / 参照: UniProt: Q13485 #3: 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: 2 |
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-試料調製
結晶 | マシュー密度: 2.13 Å3/Da / 溶媒含有率: 42.16 % |
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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: 7.5 詳細: 50 mM Tris-HCl, 0-15 mM magnesium chloride, 5-15% ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-データ収集
回折 |
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放射光源 |
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検出器 |
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放射 |
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放射波長 |
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反射 | 解像度: 2.5→100 Å / Num. all: 21793 / Num. obs: 20128 / % possible obs: 92.4 % / 冗長度: 5.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 27.5 | ||||||||||||||||||
反射 シェル | 解像度: 2.5→2.6 Å / Mean I/σ(I) obs: 3 / Num. unique all: 1110 / % possible all: 87.2 |
-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 ENTRY 1KHX 解像度: 2.6→100 Å / Isotropic thermal model: restrained / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber
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原子変位パラメータ | Biso mean: 64 Å2 | |||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.6→100 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.6→2.69 Å
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