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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: 1n8e | ||||||
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タイトル | Fragment Double-D from Human Fibrin | ||||||
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![]() | BLOOD CLOTTING / Cross-linked fibrin / D:D interfaces / crystal packing | ||||||
機能・相同性 | ![]() platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) ...platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein secretion / protein polymerization / cellular response to interleukin-1 / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / cell adhesion molecule binding / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / 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) / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Platelet degranulation / protein-macromolecule adaptor activity / protein-folding chaperone binding / ER-Phagosome pathway / cell cortex / protein-containing complex assembly / collagen-containing extracellular matrix / adaptive immune response / blood microparticle / positive regulation of ERK1 and ERK2 cascade / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / signaling receptor binding / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Yang, Z. / Pandi, L. / Doolittle, R.F. | ||||||
![]() | ![]() タイトル: The Crystal Structure of Fragment Double-D from Cross-Linked Lamprey Fibrin Reveals Isopeptide Linkages across an Unexpected D-D Interface 著者: Yang, Z. / Pandi, L. / Doolittle, R.F. #1: ![]() タイトル: Crystal Structure of Fragment Double-D from Human Fibrin with Two Different Bound Ligands 著者: Everse, S.J. / Spraggon, G. / Veerapandian, L. / Riley, M. / Doolittle, R.F. | ||||||
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 | ![]() | 55.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 31.1 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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要素
#1: タンパク質 | 分子量: 10517.244 Da / 分子数: 2 / 断片: double-D alpha chain / 由来タイプ: 天然 / 詳細: Fibrinogen prepared from blood bank plasma / 由来: (天然) ![]() #2: タンパク質 | 分子量: 37691.992 Da / 分子数: 2 / 断片: double-D beta chain / 由来タイプ: 天然 / 詳細: Fibrinogen prepared from blood bank plasma / 由来: (天然) ![]() #3: タンパク質 | 分子量: 36693.754 Da / 分子数: 2 / 断片: double-D gamma chain / 由来タイプ: 天然 / 詳細: Fibrinogen prepared from blood bank plasma / 由来: (天然) ![]() |
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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: 2.88 Å3/Da / 溶媒含有率: 57.27 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5 詳細: PEG-3350, 50 mM Tris, 7.5 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 1999年2月2日 |
放射 | モノクロメーター: wiggler / 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: 0.98 Å / 相対比: 1 |
反射 | 解像度: 4.5→30 Å / Num. all: 12247 / Num. obs: 10214 / % possible obs: 83.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.138 |
反射 シェル | 解像度: 4.5→4.6 Å / % possible all: 53.3 |
反射 | *PLUS Num. measured all: 71273 |
反射 シェル | *PLUS % possible obs: 53.3 % |
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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: fragment D of 1FZC 解像度: 4.5→30 Å / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber / 詳細: The coordinates contain C-Alphas only.
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精密化ステップ | サイクル: LAST / 解像度: 4.5→30 Å
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ソフトウェア | *PLUS 名称: CNS / バージョン: 1 / 分類: refinement | ||||||||||||||||||||
精密化 | *PLUS 最低解像度: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||
原子変位パラメータ | *PLUS |