+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1s4g | ||||||
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タイトル | Somatomedin-B Domain of human plasma vitronectin. | ||||||
要素 | Vitronectinビトロネクチン | ||||||
キーワード | CELL ADHESION (細胞接着) / Somatomedin B domain / disulfide knot / vitronectin (ビトロネクチン) | ||||||
機能・相同性 | 機能・相同性情報 rough endoplasmic reticulum lumen / smooth muscle cell-matrix adhesion / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / scavenger receptor activity / negative regulation of endopeptidase activity / protein complex involved in cell-matrix adhesion / negative regulation of blood coagulation / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway ...rough endoplasmic reticulum lumen / smooth muscle cell-matrix adhesion / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / scavenger receptor activity / negative regulation of endopeptidase activity / protein complex involved in cell-matrix adhesion / negative regulation of blood coagulation / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / Molecules associated with elastic fibres / extracellular matrix structural constituent / cell adhesion mediated by integrin / Syndecan interactions / polysaccharide binding / positive regulation of wound healing / positive regulation of smooth muscle cell migration / endodermal cell differentiation / oligodendrocyte differentiation / protein polymerization / 基底膜 / ECM proteoglycans / Integrin cell surface interactions / negative regulation of fibrinolysis / regulation of cell adhesion / collagen binding / extracellular matrix organization / cell-matrix adhesion / Regulation of Complement cascade / liver regeneration / positive regulation of receptor-mediated endocytosis / Golgi lumen / positive regulation of peptidyl-tyrosine phosphorylation / 遊走 / integrin binding / positive regulation of protein binding / heparin binding / collagen-containing extracellular matrix / blood microparticle / 細胞接着 / 免疫応答 / intracellular membrane-bounded organelle / 小胞体 / extracellular space / extracellular exosome / extracellular region / identical protein binding 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 溶液NMR / simulated annealing | ||||||
データ登録者 | Mayasundari, A. / Whittemore, N.A. / Serpersu, E.H. / Peterson, C.B. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2004 タイトル: The solution structure of the N-terminal domain of human vitronectin: proximal sites that regulate fibrinolysis and cell migration 著者: Mayasundari, A. / Whittemore, N.A. / Serpersu, E.H. / Peterson, C.B. | ||||||
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 | 1s4g.cif.gz | 297 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1s4g.ent.gz | 255.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1s4g.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/s4/1s4g ftp://data.pdbj.org/pub/pdb/validation_reports/s4/1s4g | 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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NMR アンサンブル |
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-要素
#1: タンパク質 | 分子量: 5824.493 Da / 分子数: 1 / 断片: Somatomedin B / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 組織: plasma / 参照: UniProt: P04004 |
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#2: 化合物 | ChemComp-OH / |
-実験情報
-実験
実験 | 手法: 溶液NMR | ||||||||||||||||
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NMR実験 |
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-試料調製
詳細 | 内容: Isolated from human plasma vitronectin by CNBr cleavage |
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試料状態 | イオン強度: low / pH: 4.4 / 温度: 298 K |
-NMR測定
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M |
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放射波長 | 相対比: 1 |
NMRスペクトロメーター | タイプ: Varian INOVA / 製造業者: Varian / モデル: INOVA / 磁場強度: 600 MHz |
-解析
NMR software |
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精密化 | 手法: simulated annealing / ソフトェア番号: 1 詳細: NOE cross-peak intensities were converted into distance restraints as follows: strong, 1.8-2.7 ; medium, 1.8-3.4 ; weak, 1.8-4.5 , and very weak 1.8-6.0. An additional 1.0 was added to upper ...詳細: NOE cross-peak intensities were converted into distance restraints as follows: strong, 1.8-2.7 ; medium, 1.8-3.4 ; weak, 1.8-4.5 , and very weak 1.8-6.0. An additional 1.0 was added to upper limits involving methyl protons, 0.5 for methylene protons and 2.3 for degenerate Hd and He protons of tyrosines and phenylalanines. Also, a 0.2 was added to the upper limits of NOEs involving amide protons. Backbone F angles were restrained to -120 50 for 3JHNHa = 8-9 Hz, and -120 40 for JHNHa > 9Hz. A restraint of 100 80 was also applied to F angle for residues that show stronger NHi-Hai-1 NOE than the intraresidue NH-Ha NOE. A total of 329 NOE restraints and 18 F restraints were used in structure determination. Random structures were generated by subjecting the peptide to an initial 10000-step minimization at 298K. The temperature was then raised gradually to 1000K during a 1000 step dynamics simulation. The peptide was subjected to minimization and a 10ps dynamics at 1000K. The NMR-derived restraints were then imposed on the peptide and the peptide was slowly annealed to 298K in a 100ps trajectory. Finally, the structures were subjected to further minimization at 298K. The force constant for the distance restraints was 100 kcal/mol 2 and the dielectric constant was 4. | ||||||||||||||||||||||||||||
代表構造 | 選択基準: closest to the average | ||||||||||||||||||||||||||||
NMRアンサンブル | コンフォーマー選択の基準: structures with favorable non-bond energy 計算したコンフォーマーの数: 60 / 登録したコンフォーマーの数: 20 |