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基本情報
登録情報 | データベース: PDB / ID: 3hxq | ||||||
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タイトル | Crystal Structure of Von Willebrand Factor (VWF) A1 Domain in Complex with DNA Aptamer ARC1172, an Inhibitor of VWF-Platelet Binding | ||||||
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![]() | BLOOD CLOTTING/BLOOD CLOTTING REGULATOR / ARC1779 / VWF / Platelet Glycoprotein Ib / Aptamer / ARC1772 / Blood coagulation / Cell adhesion / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Extracellular matrix / Glycoprotein / Hemostasis / Isopeptide bond / Secreted / von Willebrand disease / BLOOD CLOTTING-BLOOD CLOTTING REGULATOR COMPLEX | ||||||
機能・相同性 | ![]() Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet 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 / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / protein-folding chaperone binding / protease binding / collagen-containing extracellular matrix / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Huang, R.H. / Sadler, J.E. / Fremont, D.H. / Diener, J.L. / Schaub, R.G. | ||||||
![]() | ![]() タイトル: A structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1. 著者: Huang, R.H. / Fremont, D.H. / Diener, J.L. / Schaub, R.G. / Sadler, J.E. #1: ジャーナル: Circulation / 年: 2007 タイトル: First-in-human evaluation of anti von Willebrand factor therapeutic aptamer ARC1779 in healthy volunteers. 著者: Gilbert, J.C. / DeFeo-Fraulini, T. / Hutabarat, R.M. / Horvath, C.J. / Merlino, P.G. / Marsh, H.N. / Healy, J.M. / Boufakhreddine, S. / Holohan, T.V. / Schaub, R.G. #2: ジャーナル: J.Thromb.Haemost. / 年: 2009 タイトル: Inhibition of von Willebrand factor-mediated platelet activation and thrombosis by the anti-von Willebrand factor A1-domain aptamer ARC1779. 著者: Diener, J.L. / Daniel Lagasse, H.A. / Duerschmied, D. / Merhi, Y. / Tanguay, J.F. / Hutabarat, R. / Gilbert, J. / Wagner, D.D. / Schaub, 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 | ![]() | 147.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 113.5 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
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リンク
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集合体
登録構造単位 | ![]()
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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: 23889.627 Da / 分子数: 1 断片: von Willebrand factor (VWF) A1 Domain (residues 1260-1468) 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#2: DNA鎖 | 分子量: 12884.188 Da / 分子数: 1 / 断片: Aptamer ARC1172 / 由来タイプ: 合成 詳細: ARC1172 is a DNA oligonucleotides that bind specific target molecules, identified by selection in vitro from large random sequence libraries (termed SELEX: systematic evolution of ligands by ...詳細: ARC1172 is a DNA oligonucleotides that bind specific target molecules, identified by selection in vitro from large random sequence libraries (termed SELEX: systematic evolution of ligands by exponential enrichment) |
#3: 水 | ChemComp-HOH / |
構成要素の詳細 | AUTHOR STATE THAT THE LAST RESIDUE OF THE DNA POLYMER IS AN INVERTED-DT WHICH IS NOT MODELED DUE TO ...AUTHOR STATE THAT THE LAST RESIDUE OF THE DNA POLYMER IS AN INVERTED-DT WHICH IS NOT MODELED DUE TO DISORDER. 3' INVERTED DT IS LINKED TO THE PHOSPHATE GROUP OF ITS PREVIOUS RESIDUE BY THE THIRD CARBON ATOMS OF THE SUGAR RINGS. |
-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: 2.41 Å3/Da / 溶媒含有率: 49.06 % |
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結晶化 | 温度: 293 K / pH: 4.6 詳細: 0.2 M NH4Ac, 0.1 M NaAc, 30% PEG4000, pH 4.6, EVAPORATION, temperature 293K |
-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: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 2008年3月17日 |
放射 | モノクロメーター: GRAPHITE / 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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.694→38 Å / Num. obs: 9819 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / 冗長度: 6.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2 |
反射 シェル | 解像度: 2.69→2.8 Å / 冗長度: 4 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.8 / % possible all: 83.9 |
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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: 3HXO 解像度: 2.694→38 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.44 / σ(F): 1.5 / 位相誤差: 27.15 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 44.193 Å2 / ksol: 0.311 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 170.21 Å2 / Biso mean: 63.419 Å2 / Biso min: 17.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.694→38 Å
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拘束条件 |
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LS精密化 シェル |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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