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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: 6rhc | ||||||
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タイトル | Fragment AZ-003 binding at the TAZpS89/14-3-3 sigma interface | ||||||
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![]() | PEPTIDE BINDING PROTEIN / protein protein interaction / fragment soaking / stabilization | ||||||
機能・相同性 | ![]() kidney morphogenesis / regulation of metanephric nephron tubule epithelial cell differentiation / Physiological factors / RUNX3 regulates YAP1-mediated transcription / mesenchymal cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / stem cell division / tissue homeostasis / hippo signaling ...kidney morphogenesis / regulation of metanephric nephron tubule epithelial cell differentiation / Physiological factors / RUNX3 regulates YAP1-mediated transcription / mesenchymal cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / stem cell division / tissue homeostasis / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / SMAD protein signal transduction / glomerulus development / Signaling by Hippo / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / negative regulation of fat cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / RUNX2 regulates osteoblast differentiation / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / cilium assembly / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / positive regulation of osteoblast differentiation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of epithelial to mesenchymal transition / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / protein sequestering activity / protein kinase A signaling / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / negative regulation of protein phosphorylation / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Downregulation of SMAD2/3:SMAD4 transcriptional activity / transcription coregulator activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of protein kinase activity / negative regulation of canonical Wnt signaling pathway / multicellular organism growth / positive regulation of protein localization to nucleus / osteoblast differentiation / transcription corepressor activity / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / positive regulation of cell growth / transcription regulator complex / transcription coactivator activity / nuclear body / regulation of cell cycle / protein ubiquitination / cadherin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Genet, S. / Wolter, M. / Guillory, X. / Somsen, B. / Leysen, S. / Castaldi, P. / Ottmann, C. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Fragment-based Differential Targeting of PPI Stabilizer Interfaces. 著者: Guillory, X. / Wolter, M. / Leysen, S. / Neves, J.F. / Kuusk, A. / Genet, S. / Somsen, B. / Morrow, J.K. / Rivers, E. / van Beek, L. / Patel, J. / Goodnow, R. / Schoenherr, H. / Fuller, N. / ...著者: Guillory, X. / Wolter, M. / Leysen, S. / Neves, J.F. / Kuusk, A. / Genet, S. / Somsen, B. / Morrow, J.K. / Rivers, E. / van Beek, L. / Patel, J. / Goodnow, R. / Schoenherr, H. / Fuller, N. / Cao, Q. / Doveston, R.G. / Brunsveld, L. / Arkin, M.R. / Castaldi, P. / Boyd, H. / Landrieu, I. / Chen, H. / Ottmann, C. | ||||||
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 | ![]() | 73.2 KB | 表示 | ![]() |
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PDB形式 | ![]() | 51.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 6r5lC ![]() 6rjlC ![]() 6rjqC ![]() 6rjzC ![]() 6rk8C ![]() 6rkiC ![]() 6rkkC ![]() 6rkmC ![]() 6rl3C ![]() 6rl4C ![]() 6rl6C ![]() 6rm5C ![]() 6rm7C ![]() 6rp6C ![]() 6rwhC ![]() 6rwiC ![]() 6rwsC ![]() 6rwuC ![]() 6rx2C ![]() 6s39C ![]() 6s3cC ![]() 6s40C ![]() 6s9qC ![]() 6sinC ![]() 6sioC ![]() 6sipC ![]() 6siqC ![]() 6slvC ![]() 6slwC ![]() 6slxC ![]() 3mhrS S: 精密化の開始モデル C: 同じ文献を引用 ( |
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類似構造データ |
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リンク
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集合体
登録構造単位 | ![]()
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1 | ![]()
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単位格子 |
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Components on special symmetry positions |
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要素
-タンパク質 / タンパク質・ペプチド , 2種, 2分子 AP
#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) ![]() ![]() ![]() |
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#2: タンパク質・ペプチド | 分子量: 1422.439 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) ![]() |
-非ポリマー , 4種, 300分子 ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K48.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K48.gif)
![](data/chem/img/HOH.gif)
#3: 化合物 | #4: 化合物 | #5: 化合物 | ChemComp-K48 / | #6: 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: 2.67 Å3/Da / 溶媒含有率: 53.99 % |
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結晶化 | 温度: 277.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: Protein and peptide were mixed at a 1:2 molar stoichiometry with a final protein concentration of 12 mg/mL in crystallization buffer. This was used during hanging-drop crystallization in a 1: ...詳細: Protein and peptide were mixed at a 1:2 molar stoichiometry with a final protein concentration of 12 mg/mL in crystallization buffer. This was used during hanging-drop crystallization in a 1:1 ratio with 0.1 M HEPES pH 7.5, 0.2 M CaCl2, 5% glycerol, 2 mM BME and 28% PEG400. Crystals were grown within 10 days at 4 C and fragment soaking was performed on crystals of 10 days and older by adding 0.2 uL of a 100 mM stock solution in dimethyl sulfoxide to 2 uL drops containing multiple crystals. |
-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: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2018年10月28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: 1.033191 Å / 相対比: 1 |
反射 | 解像度: 1.2→41.83 Å / Num. obs: 89802 / % possible obs: 99.3 % / 冗長度: 12.8 % / CC1/2: 0.997 / Rrim(I) all: 0.113 / Net I/σ(I): 11.3 |
反射 シェル | 解像度: 1.2→1.22 Å / 冗長度: 12.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4345 / CC1/2: 0.575 / Rrim(I) all: 0.937 / % possible all: 97.3 |
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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: 3MHR 解像度: 1.2→41.83 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.684 / SU ML: 0.029 / 交差検証法: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.039 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 14.636 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.2→41.83 Å
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拘束条件 |
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