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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 6hil | ||||||
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タイトル | X-ray structure of TEAD1(Y421H mutant) complexed with YAP(wildtype): Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy | ||||||
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![]() | TRANSCRIPTION / OTHER / TRANSCRIPTION FACTOR | ||||||
機能・相同性 | ![]() enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / regulation of stem cell proliferation / hippo signaling / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / proline-rich region binding / Signaling by Hippo / negative regulation of epithelial cell differentiation / organ growth / interleukin-6-mediated signaling pathway / positive regulation of stem cell population maintenance / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / regulation of neurogenesis / canonical Wnt signaling pathway / vasculogenesis / embryonic organ development / positive regulation of osteoblast differentiation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / Nuclear signaling by ERBB4 / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / epithelial cell proliferation / positive regulation of epithelial cell proliferation / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / transcription corepressor activity / sequence-specific double-stranded DNA binding / cell-cell junction / positive regulation of canonical Wnt signaling pathway / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription factor binding / transcription regulator complex / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / DNA damage response / chromatin binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Kallen, J. | ||||||
![]() | ![]() タイトル: Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy. 著者: Bokhovchuk, F. / Mesrouze, Y. / Izaac, A. / Meyerhofer, M. / Zimmermann, C. / Fontana, P. / Schmelzle, T. / Erdmann, D. / Furet, P. / Kallen, J. / Chene, P. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 207.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 165.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 499.2 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 515.6 KB | 表示 | |
XML形式データ | ![]() | 37.3 KB | 表示 | |
CIF形式データ | ![]() | 50.3 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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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: 25223.740 Da / 分子数: 4 / 断片: C-terminal domain, YAP binding domain / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質・ペプチド | 分子量: 4650.309 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() #3: 化合物 | ChemComp-MYR / #4: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.1 Å3/Da / 溶媒含有率: 41.4 % |
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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: 5 / 詳細: 22% (w/v) PEG3350, 0.2M Na Malonate |
-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: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2018年4月13日 |
放射 | モノクロメーター: SI 111 channel / 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 Å / 相対比: 1 |
反射 | 解像度: 2.3→19.9 Å / Num. obs: 41611 / % possible obs: 95.5 % / 冗長度: 1.8 % / Biso Wilson estimate: 51.3 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.0998 / Rrim(I) all: 0.065 / Net I/σ(I): 10.9 / Num. measured all: 74068 |
反射 シェル | 解像度: 2.3→2.36 Å / 冗長度: 1.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.2 / Rpim(I) all: 0.702 / Rrim(I) all: 0.804 / % possible all: 95.4 |
-位相決定
位相決定 | 手法: ![]() |
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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: ![]() 開始モデル: 3KYS 解像度: 2.3→19.9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.755 / SU ML: 0.25 / SU R Cruickshank DPI: 0.5941 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.594 / ESU R Free: 0.286 詳細: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 133.82 Å2 / Biso mean: 48.846 Å2 / Biso min: 19.82 Å2
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精密化ステップ | サイクル: final / 解像度: 2.3→19.9 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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