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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: 3zrz | ||||||
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タイトル | Crystal structure of the second and third fibronectin F1 modules in complex with a fragment of Streptococcus pyogenes SfbI-5 | ||||||
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![]() | CELL ADHESION / PRTF / BETA ZIPPER | ||||||
機能・相同性 | ![]() negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking ...negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / biological process involved in interaction with symbiont / proteoglycan binding / Molecules associated with elastic fibres / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / endoplasmic reticulum-Golgi intermediate compartment / : / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / collagen binding / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / extracellular matrix / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / regulation of protein phosphorylation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / GPER1 signaling / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / nervous system development / heart development / heparin binding / regulation of cell shape / protease binding / Interleukin-4 and Interleukin-13 signaling / angiogenesis / collagen-containing extracellular matrix / membrane => GO:0016020 / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Norris, N.C. / Bingham, R.J. / Potts, J.R. | ||||||
![]() | ![]() タイトル: Structural and Functional Analysis of the Tandem Beta-Zipper Interaction of a Streptococcal Protein with Human Fibronectin. 著者: Norris, N.C. / Bingham, R.J. / Harris, G. / Speakman, A. / Jones, R.P.O. / Leech, A. / Turkenburg, J.P. / Potts, J.R. | ||||||
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 | ![]() | 61.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 44.3 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 | ![]() 2rkzS S: 精密化の開始モデル |
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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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2 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 10120.389 Da / 分子数: 2 / 断片: SECOND AND THIRD F1 MODULES, RESIDUES 93-182 / 由来タイプ: 組換発現 詳細: IN BOTH A AND B THERE ARE DISULFIDE BONDS BETWEEN RESIDUES C 97 AND C 125, C 123 AND C 135, C 141 AND C 169, C 167 AND C 179 由来: (組換発現) ![]() ![]() #2: タンパク質・ペプチド | 分子量: 1952.148 Da / 分子数: 2 / 断片: RESIDUES 560-577 / 由来タイプ: 合成 詳細: ACETYLATED ON THE N-TERMINUS AND AMIDATED ON THE C-TERMINUS 由来: (合成) ![]() 参照: UniProt: Q01924, UniProt: Q711B0*PLUS #3: 化合物 | ChemComp-SO4 / | #4: 化合物 | #5: 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: 2.45 Å3/Da / 溶媒含有率: 49.7 % 解説: 2F1 AND 3F1 FROM 2RKZ WERE SEARCHED SEPARATELY IN PHASER. THE PEPTIDE FROM THIS STRUCTURE WAS NOT USED. |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 詳細: CRYSTALS OF THE PROTEIN/PEPTIDE COMPLEX (0.3 MM/3.5 MM, PH 7.7) WERE GROWN USING SITTING DROP VAPOUR DIFFUSION FROM A 1:1 DILUTION WITH WELL SOLUTION (0.1 M TRIS PH 7.0, 1.5 M (NH4)2SO4 AT 18 DEGREES CENTIGRADE |
-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: ![]() ![]() ![]() |
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2008年3月8日 / 詳細: BENT CYLINDRICAL MIRRORS |
放射 | モノクロメーター: SI(111) / 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: 0.9804 Å / 相対比: 1 |
反射 | 解像度: 1.7→28.22 Å / Num. obs: 25333 / % possible obs: 100 % / Observed criterion σ(I): 1.9 / 冗長度: 6.1 % / Biso Wilson estimate: 22.64 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.4 |
反射 シェル | 解像度: 1.7→1.79 Å / 冗長度: 6.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
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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: PDB ENTRY 2RKZ 解像度: 1.7→26.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.041 / SU ML: 0.068 / 交差検証法: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.108 / 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: 23.575 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.7→26.45 Å
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拘束条件 |
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