+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1g88 | ||||||
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タイトル | S4AFL3ARG515 MUTANT | ||||||
要素 | SMAD4 | ||||||
キーワード | TRANSCRIPTION (転写 (生物学)) / transcriptional factor (転写因子) / L3 loop mutant | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer ...positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / positive regulation of luteinizing hormone secretion / regulation of hair follicle development / sebaceous gland development / SMAD protein complex / formation of anatomical boundary / epithelial cell migration / RUNX2 regulates bone development / positive regulation of follicle-stimulating hormone secretion / 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 / response to transforming growth factor beta / secondary palate development / FOXO-mediated transcription of cell cycle genes / 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 / atrioventricular canal development / cardiac conduction system development / positive regulation of extracellular matrix assembly / Germ layer formation at gastrulation / sulfate binding / Signaling by BMP / Formation of definitive endoderm / cellular response to BMP stimulus / activin receptor signaling pathway / outflow tract septum morphogenesis / Signaling by Activin / SMAD protein signal transduction / Signaling by NODAL / cardiac muscle hypertrophy in response to stress / gastrulation with mouth forming second / I-SMAD binding / neural crest cell differentiation / endothelial cell activation / Cardiogenesis / RUNX3 regulates CDKN1A transcription / branching involved in ureteric bud morphogenesis / embryonic digit morphogenesis / adrenal gland development / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / seminiferous tubule development / positive regulation of cardiac muscle cell apoptotic process / positive regulation of transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling activates SMADs / single fertilization / R-SMAD binding / uterus development / positive regulation of SMAD protein signal transduction / developmental growth / anatomical structure morphogenesis / 上皮間葉転換 / positive regulation of epithelial to mesenchymal transition / BMP signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ovarian follicle development / extrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / cellular response to transforming growth factor beta stimulus / collagen binding / transforming growth factor beta receptor signaling pathway / transcription corepressor binding / 軸索誘導 / cellular response to glucose stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of canonical Wnt signaling pathway / transcription coactivator binding / negative regulation of cell growth / negative regulation of ERK1 and ERK2 cascade / negative regulation of protein catabolic process / osteoblast differentiation / positive regulation of miRNA transcription / 精子形成 / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / cell population proliferation / intracellular iron ion homeostasis / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 3 Å | ||||||
データ登録者 | Chako, B.M. / Qin, B. / Lam, S.S. / Correia, J.J. / Lin, K. | ||||||
引用 | ジャーナル: Nat.Struct.Biol. / 年: 2001 タイトル: The L3 loop and C-terminal phosphorylation jointly define Smad protein trimerization. 著者: Chacko, B.M. / Qin, B. / Correia, J.J. / Lam, S.S. / de Caestecker, M.P. / 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 | 1g88.cif.gz | 142.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1g88.ent.gz | 113.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1g88.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/g8/1g88 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/1g88 | HTTPS FTP |
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-関連構造データ
関連構造データ | |
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類似構造データ |
-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: 29348.332 Da / 分子数: 3 / 断片: SMAD4 ACTIVE FRAGMENT / 変異: R515S / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q13485 |
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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: 2.74 Å3/Da / 溶媒含有率: 55.09 % | ||||||||||||||||||||
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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: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
結晶化 | *PLUS pH: 7.5 / 手法: unknown | ||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 298 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU |
検出器 | タイプ: RIGAKU / 検出器: IMAGE PLATE / 日付: 2000年3月1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 | 相対比: 1 |
反射 | 解像度: 3→50 Å / Num. all: 72845 / Num. obs: 19552 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5.5 / 冗長度: 3.72 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.5 |
反射 シェル | 解像度: 3→3.11 Å / 冗長度: 3 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 5.5 / % possible all: 88 |
反射 | *PLUS 最高解像度: 3 Å / 最低解像度: 50 Å / Num. measured all: 72845 |
反射 シェル | *PLUS 最高解像度: 3 Å / % possible obs: 88 % / Mean I/σ(I) obs: 2.3 |
-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: 3→40.5 Å / Data cutoff high absF: 191639.16 / Data cutoff low absF: 0 / 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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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 12 Å2 / ksol: 0.323 e/Å3 | |||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 26.4 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.43 Å | |||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 3→40.5 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 3→3.19 Å / Total num. of bins used: 6 /
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Xplor file |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 0.9 / 分類: refinement | |||||||||||||||||||||||||
精密化 | *PLUS σ(F): 0 / % reflection Rfree: 10 % | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 26.4 Å2 | |||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rwork: 0.276 |