+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6df6 | ||||||
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タイトル | Crystal structure of estrogen receptor alpha in complex with receptor degrader 16ab | ||||||
要素 | Estrogen receptorエストロゲン受容体 | ||||||
キーワード | NUCLEAR PROTEIN / ERA / antagonist (受容体拮抗薬) / inverse agonist (受容体逆作動薬) / receptor (受容体) / breast cancer / degrader / ligand (リガンド) / estrogen receptor (エストロゲン受容体) | ||||||
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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation ...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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / androgen metabolic process / TFIIB-class transcription factor binding / steroid hormone mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / 14-3-3 protein binding / transcription corepressor binding / negative regulation of miRNA transcription / cellular response to estradiol stimulus / transcription coregulator binding / 細胞分化 / nuclear estrogen receptor binding / positive regulation of nitric-oxide synthase activity / ユークロマチン / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / クロマチンリモデリング / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / クロマチン / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / ゴルジ体 / negative regulation of transcription by RNA polymerase II / enzyme binding / シグナル伝達 / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / 核質 / 生体膜 / identical protein binding / 細胞核 / 細胞膜 / 細胞質基質 / 細胞質 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: 2.5 Å | ||||||
データ登録者 | Kiefer, J.R. / Vinogradova, M. / Liang, J. / Zhang, B. / Ortwine, D.F. / Nettles, K.W. / Nwachukwu, J.C. | ||||||
引用 | ジャーナル: Bioorg. Med. Chem. Lett. / 年: 2019 タイトル: Unexpected equivalent potency of a constrained chromene enantiomeric pair rationalized by co-crystal structures in complex with estrogen receptor alpha. 著者: Zhang, B. / Kiefer, J.R. / Blake, R.A. / Chang, J.H. / Hartman, S. / Ingalla, E.R. / Kleinheinz, T. / Mody, V. / Nannini, M. / Ortwine, D.F. / Ran, Y. / Sambrone, A. / Sampath, D. / ...著者: Zhang, B. / Kiefer, J.R. / Blake, R.A. / Chang, J.H. / Hartman, S. / Ingalla, E.R. / Kleinheinz, T. / Mody, V. / Nannini, M. / Ortwine, D.F. / Ran, Y. / Sambrone, A. / Sampath, D. / Vinogradova, M. / Zhong, Y. / Nwachukwu, J.C. / Nettles, K.W. / Lai, T. / Liao, J. / Zheng, X. / Chen, H. / Wang, X. / Liang, J. | ||||||
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 | 6df6.cif.gz | 193.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6df6.ent.gz | 154.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6df6.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/df/6df6 ftp://data.pdbj.org/pub/pdb/validation_reports/df/6df6 | 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
#1: タンパク質 | 分子量: 31980.295 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ESR1, ESR, NR3A1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P03372 #2: 化合物 | ChemComp-G8Y / ( #3: 化合物 | #4: 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: 1.99 Å3/Da / 溶媒含有率: 38.14 % |
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結晶化 | 温度: 292 K / 手法: 蒸気拡散法, ハンギングドロップ法 詳細: grid of PEG 3350 vs. MgCl2 with a buffer of Bis-TRIS at pH 6-6.5 |
-データ収集
回折 | 平均測定温度: 93 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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放射光源 | 由来: シンクロトロン / サイト: ALS / ビームライン: 5.0.2 / 波長: 1.00004 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2015年2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: 1.00004 Å / 相対比: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 2.5→35 Å / Num. obs: 27230 / % possible obs: 81.1 % / 冗長度: 1.7 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.077 / Rrim(I) all: 0.108 / Χ2: 1.009 / Net I/σ(I): 6.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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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: 2.5→35 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.322 / SU ML: 0.365 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.399 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 115.41 Å2 / Biso mean: 54.465 Å2 / Biso min: 17.36 Å2
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精密化ステップ | サイクル: final / 解像度: 2.5→35 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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