+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3sl9 | ||||||
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タイトル | X-ray structure of Beta catenin in complex with Bcl9 | ||||||
要素 |
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キーワード | SIGNALING PROTEIN / PROTEIN BINDING (タンパク質) / Armadillo repeat (アルマジロリピート) / components of the Wnt signaling pathway / Beta catenin (Β-カテニン) | ||||||
機能・相同性 | 機能・相同性情報 myotube differentiation involved in skeletal muscle regeneration / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development ...myotube differentiation involved in skeletal muscle regeneration / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / mesenchymal stem cell differentiation / beta-catenin-ICAT complex / metanephros morphogenesis / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / neural plate development / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / negative regulation of mitotic cell cycle, embryonic / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / regulation of timing of anagen / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of centromeric sister chromatid cohesion / embryonic axis specification / endodermal cell fate commitment / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / sympathetic ganglion development / establishment of blood-retinal barrier / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / positive regulation of odontoblast differentiation / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / presynaptic active zone cytoplasmic component / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / alpha-catenin binding / flotillin complex / establishment of blood-brain barrier / Germ layer formation at gastrulation / male genitalia development / negative regulation of oligodendrocyte differentiation / fascia adherens / epithelial cell proliferation involved in prostate gland development / apicolateral plasma membrane / embryonic brain development / Formation of definitive endoderm / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / oocyte development / beta-catenin destruction complex / lung-associated mesenchyme development / Formation of axial mesoderm / cis-Golgi network / negative regulation of protein sumoylation / adherens junction assembly / embryonic heart tube development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated 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: 2.2 Å | ||||||
データ登録者 | Gupta, D. / Bienz, M. | ||||||
引用 | ジャーナル: Nat Commun / 年: 2012 タイトル: An intrinsically labile alpha-helix abutting the BCL9-binding site of beta-catenin is required for its inhibition by carnosic acid. 著者: de la Roche, M. / Rutherford, T.J. / Gupta, D. / Veprintsev, D.B. / Saxty, B. / Freund, S.M. / Bienz, M. | ||||||
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 | 3sl9.cif.gz | 158 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3sl9.ent.gz | 124 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3sl9.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/sl/3sl9 ftp://data.pdbj.org/pub/pdb/validation_reports/sl/3sl9 | 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
-タンパク質 , 2種, 8分子 ABEGCDFH
#1: タンパク質 | 分子量: 18176.174 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: Beta catenin, CTNNB, CTNNB1, OK/SW-cl.35, PRO2286 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Bl21(DE3) / 参照: UniProt: P35222 #2: タンパク質 | 分子量: 6171.756 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: BCL9 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: O00512 |
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-非ポリマー , 5種, 180分子
#3: 化合物 | ChemComp-EDO / #4: 化合物 | ChemComp-PEG / #5: 化合物 | ChemComp-IMD / #6: 化合物 | ChemComp-GOL / #7: 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: 2.87 Å3/Da / 溶媒含有率: 57.1 % |
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結晶化 | 温度: 298 K / pH: 6.5 詳細: 0.12M ethylene glycol, 1M MES 62% MES, 1M Imidazol 38%, 10% PEG 4K, 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: シンクロトロン / サイト: ESRF / ビームライン: ID14-2 / 波長: 0.93 |
検出器 | タイプ: ADSC QUANTUM 4r / 検出器: CCD / 日付: 2009年11月20日 |
放射 | モノクロメーター: DIAMOND (111), GE(220) / 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: 0.93 Å / 相対比: 1 |
反射 | 解像度: 2.2→32.07 Å / Num. obs: 54333 / % possible obs: 97.2 % / Observed criterion σ(I): -4 / 冗長度: 3.8 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1 |
反射 シェル | 解像度: 2.2→2.26 Å / 冗長度: 3.8 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 17.1 / % possible all: 97.2 |
-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: PDB ENTRY 2GL7 解像度: 2.2→29.43 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.251 / SU ML: 0.112 / 交差検証法: THROUGHOUT / σ(F): 2 / ESU R Free: 0.189 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 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: 1.4 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 40.4 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.2→29.43 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.2→2.26 Å / Total num. of bins used: 20
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