+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8aro | ||||||
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タイトル | Small molecular stabilizer for ERalpha and 14-3-3 (1080291) | ||||||
要素 |
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キーワード | STRUCTURAL PROTEIN / 14-3-3 / ERalpha / stabilization / covalent | ||||||
機能・相同性 | 機能・相同性情報 regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / positive regulation of epidermal cell differentiation / epithelial cell proliferation involved in mammary gland duct elongation / keratinocyte development / epithelial cell development / keratinization / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / Regulation of localization of FOXO transcription factors / androgen metabolic process / steroid hormone receptor signaling pathway / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / mammary gland alveolus development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / estrogen receptor signaling pathway / cellular response to estrogen stimulus / establishment of skin barrier / estrogen response element binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / : / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / nuclear receptor-mediated steroid hormone signaling pathway / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / RHO GTPases activate PKNs / negative regulation of miRNA transcription / protein localization to chromatin / 14-3-3 protein binding / cellular response to estradiol stimulus / protein sequestering activity / protein kinase A signaling / transcription coregulator binding / negative regulation of innate immune response / nitric-oxide synthase regulator activity / steroid binding / TBP-class protein binding / protein export from nucleus / ESR-mediated signaling / transcription corepressor binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / positive regulation of nitric-oxide synthase activity / stem cell proliferation / SUMOylation of intracellular receptors / Translocation of SLC2A4 (GLUT4) to the plasma membrane / stem cell differentiation / nuclear estrogen receptor binding / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / euchromatin / negative regulation of DNA-binding transcription factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / transcription coactivator binding / nuclear receptor activity / beta-catenin binding / positive regulation of fibroblast proliferation / response to estrogen / Regulation of RUNX2 expression and activity / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / PIP3 activates AKT signaling / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / protein localization / Ovarian tumor domain proteases / regulation of inflammatory response / response to estradiol / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / transcription regulator complex / Estrogen-dependent gene expression / Extra-nuclear estrogen signaling 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: 1.6 Å | ||||||
データ登録者 | Visser, E.J. / Vandenboorn, E.M.F. / Ottmann, C. | ||||||
資金援助 | オランダ, 1件
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引用 | ジャーナル: J.Am.Chem.Soc. / 年: 2023 タイトル: Structure-Based Optimization of Covalent, Small-Molecule Stabilizers of the 14-3-3 sigma /ER alpha Protein-Protein Interaction from Nonselective Fragments. 著者: Konstantinidou, M. / Visser, E.J. / Vandenboorn, E. / Chen, S. / Jaishankar, P. / Overmans, M. / Dutta, S. / Neitz, R.J. / Renslo, A.R. / Ottmann, C. / Brunsveld, L. / Arkin, M.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 | 8aro.cif.gz | 73 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8aro.ent.gz | 50.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8aro.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/ar/8aro ftp://data.pdbj.org/pub/pdb/validation_reports/ar/8aro | HTTPS FTP |
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-関連構造データ
関連構造データ | 8ai0C 8alrC 8altC 8alvC 8alwC 8am7C 8anfC 8aoyC 8apsC 8aq1C 8aqcC 8aqeC 8aqzC 8ar4C 8ar5C 8argC 8arqC 8arrC 8arwC 8arxC 8aryC 8arzC 8as1C 8at9C 8atpC 8atrC 8atsC 8au2C 8ausC 8auyC 8av3C 8av4C 8av7C 8av8C 8awgC 8axeC 8axuC 8azeC 8b39C 4jc3S S: 精密化の開始モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 26542.914 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SFN, HME1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P31947 | ||||||
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#2: タンパク質・ペプチド | 分子量: 613.596 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P03372 | ||||||
#3: 化合物 | #4: 化合物 | ChemComp-NJR / | #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
-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: 2.64 Å3/Da / 溶媒含有率: 53.45 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 詳細: 0.095 M HEPES (pH 7.3), PEG400 (24% (v/v)), 0.19 M CaCl2 and 5% (v/v) Glycerol |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: シンクロトロン / サイト: ESRF / ビームライン: ID30B / 波長: 0.976254 Å |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2021年12月3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: 0.976254 Å / 相対比: 1 |
反射 | 解像度: 1.6→45.45 Å / Num. obs: 36904 / % possible obs: 96.7 % / 冗長度: 2.9 % / CC1/2: 0.995 / Net I/σ(I): 13.6 |
反射 シェル | 解像度: 1.6→1.63 Å / Num. unique obs: 1837 / CC1/2: 0.965 |
-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: 4JC3 解像度: 1.6→45.45 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.411 / SU ML: 0.05 / 交差検証法: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.084 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1 Å / 溶媒モデル: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 14.047 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.6→45.45 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.6→1.642 Å / Total num. of bins used: 20
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