+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6gec | ||||||
---|---|---|---|---|---|---|---|
タイトル | TEAD4 (216-434) COMPLEXED WITH YAP PEPTIDE (60-100);S94A AND MYRISTOATE (COVALENTLY BOUND) AT 1.70A (P41212 CRYSTAL FORM); MYRISTOYLATION WAS DONE BY ADDING MYR-COA | ||||||
要素 |
| ||||||
キーワード | TRANSCRIPTION (転写 (生物学)) / CO-ACTIVATOR COMPLEX (コアクチベーター) / PROTEIN-PROTEIN INTERACTION (タンパク質間相互作用) | ||||||
機能・相同性 | 機能・相同性情報 trophectodermal cell fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / 接触阻害 / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription ...trophectodermal cell fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / 接触阻害 / 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 / hippo signaling / regulation of stem cell proliferation / 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 / Signaling by Hippo / proline-rich region binding / cell fate specification / muscle organ development / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of epithelial cell differentiation / organ growth / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / negative regulation of fat cell differentiation / positive regulation of Notch signaling pathway / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / progesterone receptor signaling pathway / somatic stem cell population maintenance / regulation of neurogenesis / canonical Wnt signaling pathway / 脈管形成 / 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 / 着床 / response to progesterone / epithelial cell proliferation / skeletal system development / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / transcription corepressor activity / cell-cell junction / positive regulation of canonical Wnt signaling pathway / 細胞結合 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / DNA-binding transcription factor binding / cell population proliferation / 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-templated transcription / DNA damage response / chromatin binding / クロマチン / positive regulation of gene expression / 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 / 核質 / 生体膜 / 細胞核 / 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: 1.7 Å | ||||||
データ登録者 | Kallen, J. | ||||||
引用 | ジャーナル: Protein Sci. / 年: 2018 タイトル: Adaptation of the bound intrinsically disordered protein YAP to mutations at the YAP:TEAD interface. 著者: Mesrouze, Y. / Bokhovchuk, F. / Izaac, A. / Meyerhofer, M. / Zimmermann, C. / Fontana, P. / Schmelzle, T. / Erdmann, D. / Furet, P. / Kallen, J. / Chene, P. | ||||||
履歴 |
|
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
---|
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6gec.cif.gz | 72.4 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6gec.ent.gz | 51.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6gec.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/ge/6gec ftp://data.pdbj.org/pub/pdb/validation_reports/ge/6gec | HTTPS FTP |
---|
-関連構造データ
-リンク
-集合体
登録構造単位 |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
単位格子 |
| ||||||||||||
Components on special symmetry positions |
|
-要素
#1: タンパク質 | 分子量: 25500.721 Da / 分子数: 1 / 断片: C-terminal domain, YAP binding domain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TEAD4, RTEF1, TCF13L1, TEF3 / プラスミド: pET28-derived vector / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: Q15561 |
---|---|
#2: タンパク質・ペプチド | 分子量: 4531.233 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: S94A mutant / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P46937 |
#3: 化合物 | ChemComp-MYR / |
#4: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
---|
-試料調製
結晶 | マシュー密度: 2.29 Å3/Da / 溶媒含有率: 46.23 % |
---|---|
結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 20% PEG 3350, 0.2M NaTartrate |
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: シンクロトロン / サイト: SLS / ビームライン: X10SA / 波長: 0.99994 Å |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2018年2月3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: 0.99994 Å / 相対比: 1 |
反射 | 解像度: 1.7→19.81 Å / Num. obs: 31611 / % possible obs: 99.9 % / 冗長度: 12.8 % / Biso Wilson estimate: 28.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.083 / Net I/σ(I): 21.8 / Num. measured all: 405950 |
反射 シェル | 解像度: 1.7→1.74 Å / 冗長度: 13.3 % / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 3.3 / CC1/2: 0.919 / Rrim(I) all: 1.051 / % possible all: 100 |
-位相決定
位相決定 | 手法: 分子置換 |
---|
-解析
ソフトウェア |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: 分子置換 開始モデル: 6GE3 解像度: 1.7→19.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.312 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1261 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.116 詳細: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
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: 63.03 Å2 / Biso mean: 24.409 Å2 / Biso min: 12.4 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 1.7→19.81 Å
| |||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| |||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|