+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4cud | ||||||
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タイトル | Human Notch1 EGF domains 11-13 mutant fucosylated at T466 | ||||||
要素 | NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1 | ||||||
キーワード | TRANSCRIPTION (転写 (生物学)) / METAL-BINDING / TRANSMEMBRANE (膜貫通型タンパク質) / DEVELOPMENTAL (ヒトの発達) / PROTEIN (タンパク質) / NOTCH SIGNALING PATHWAY (Notchシグナリング) / DIFFERENTIATION / PHOSPHORYLATION (リン酸化) / EGF-LIKE DOMAIN (EGF様ドメイン) / REGULATION (規制) / RECEPTOR (受容体) / ACTIVATOR / ANK REPEAT / SIGNALLING / GLYCOPROTEIN (糖タンパク質) / EXTRACELLULAR / EGF / JAGGED / NUCLEUS (細胞核) / MEMBRANE (生体膜) | ||||||
機能・相同性 | 機能・相同性情報 Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation ...Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation / cardiac chamber formation / epithelial cell fate commitment / negative regulation of pro-B cell differentiation / Pre-NOTCH Processing in the Endoplasmic Reticulum / negative regulation of inner ear auditory receptor cell differentiation / mitral valve formation / cell migration involved in endocardial cushion formation / glomerular mesangial cell development / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / inhibition of neuroepithelial cell differentiation / endocardium morphogenesis / atrioventricular node development / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / regulation of extracellular matrix assembly / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / mesenchymal cell development / epidermal cell fate specification / coronary vein morphogenesis / negative regulation of collagen biosynthetic process / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cardiac muscle hypertrophy / negative regulation of cell adhesion molecule production / interleukin-17-mediated signaling pathway / positive regulation of endothelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / endocardium development / apoptotic process involved in embryonic digit morphogenesis / positive regulation of cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / neuronal stem cell population maintenance / 再生 (生物学) / regulation of stem cell proliferation / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / calcium-ion regulated exocytosis / pulmonary valve morphogenesis / heart trabecula morphogenesis / negative regulation of biomineral tissue development / endoderm development / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / prostate gland epithelium morphogenesis / luteolysis / cardiac muscle tissue morphogenesis / ventricular trabecula myocardium morphogenesis / negative regulation of myoblast differentiation / negative regulation of cell migration involved in sprouting angiogenesis / transcription regulator activator activity / positive regulation of BMP signaling pathway / tube formation / negative regulation of stem cell differentiation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of keratinocyte differentiation / astrocyte differentiation / inflammatory response to antigenic stimulus / positive regulation of Ras protein signal transduction / negative regulation of ossification 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: 1.85 Å | ||||||
データ登録者 | Taylor, P. / Takeuchi, H. / Sheppard, D. / Chillakuri, C. / Lea, S.M. / Haltiwanger, R.S. / Handford, P.A. | ||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2014 タイトル: Fringe-Mediated Extension of O-Linked Fucose in the Ligand-Binding Region of Notch1 Increases Binding to Mammalian Notch Ligands. 著者: Taylor, P. / Takeuchi, H. / Sheppard, D. / Chillakuri, C. / Lea, S.M. / Haltiwanger, R.S. / Handford, P.A. | ||||||
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 | 4cud.cif.gz | 41.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4cud.ent.gz | 26.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4cud.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/cu/4cud ftp://data.pdbj.org/pub/pdb/validation_reports/cu/4cud | 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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1 |
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単位格子 |
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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 14857.604 Da / 分子数: 1 / 断片: EGF 11-13, RESIDUES 410-526 / 由来タイプ: 組換発現 / 詳細: O-FUCOSE MONOSACCHARIDE AT T466 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P46531 | ||
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#2: 糖 | ChemComp-FUC / | ||
#3: 化合物 | ChemComp-CA / #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 |
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-試料調製
結晶 | マシュー密度: 2.21 Å3/Da / 溶媒含有率: 44.3 % / 解説: NONE |
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結晶化 | pH: 6 / 詳細: pH 6.0 |
-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: Diamond / ビームライン: I04-1 / 波長: 0.917 |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2012年3月9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: 0.917 Å / 相対比: 1 |
反射 | 解像度: 1.85→24.14 Å / Num. obs: 10837 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / 冗長度: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 0 |
反射 シェル | 解像度: 1.85→1.9 Å / 冗長度: 5.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / % possible all: 95.3 |
-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 2VJ3 解像度: 1.85→24.14 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.319 / SU ML: 0.101 / 交差検証法: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.151 / 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: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 23.172 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.85→24.14 Å
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拘束条件 |
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