+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 9cth | ||||||||||||||||||
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タイトル | Preliminary map of the Prothrombin-prothrombinase complex on nano discs | ||||||||||||||||||
要素 |
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キーワード | BLOOD CLOTTING / Coagulation / Prothrombin / Prothrombinase / nanodisc / complex | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 response to vitamin K / coagulation factor Xa / platelet alpha granule / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / blood circulation / COPII-mediated vesicle transport / Extrinsic Pathway of Fibrin Clot Formation ...response to vitamin K / coagulation factor Xa / platelet alpha granule / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / blood circulation / COPII-mediated vesicle transport / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / COPII-coated ER to Golgi transport vesicle / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of TOR signaling / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / platelet alpha granule lumen / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / lipopolysaccharide binding / Post-translational protein phosphorylation / growth factor activity / positive regulation of insulin secretion / phospholipid binding / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / extracellular vesicle / Platelet degranulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of cell migration / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / copper ion binding / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.47 Å | ||||||||||||||||||
データ登録者 | Stojanovski, B.M. / Mohammed, B.M. / Di Cera, E. | ||||||||||||||||||
資金援助 | 米国, 5件
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引用 | ジャーナル: Subcell Biochem / 年: 2024 タイトル: The Prothrombin-Prothrombinase Interaction. 著者: Bosko M Stojanovski / Bassem M Mohammed / Enrico Di Cera / 要旨: The hemostatic response to vascular injury entails a sequence of proteolytic events where several inactive zymogens of the trypsin family are converted to active proteases. The cascade starts with ...The hemostatic response to vascular injury entails a sequence of proteolytic events where several inactive zymogens of the trypsin family are converted to active proteases. The cascade starts with exposure of tissue factor from the damaged endothelium and culminates with conversion of prothrombin to thrombin in a reaction catalyzed by the prothrombinase complex composed of the enzyme factor Xa, cofactor Va, Ca, and phospholipids. This cofactor-dependent activation is paradigmatic of analogous reactions of the blood coagulation and complement cascades, which makes elucidation of its molecular mechanism of broad significance to the large class of trypsin-like zymogens to which prothrombin belongs. Because of its relevance as the most important reaction in the physiological response to vascular injury, as well as the main trigger of pathological thrombotic complications, the mechanism of prothrombin activation has been studied extensively. However, a molecular interpretation of this mechanism has become available only recently from important developments in structural biology. Here we review current knowledge on the prothrombin-prothrombinase interaction and outline future directions for the study of this key reaction of the coagulation cascade. | ||||||||||||||||||
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 | 9cth.cif.gz | 417.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb9cth.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 9cth.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
文書・要旨 | 9cth_validation.pdf.gz | 1.5 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 9cth_full_validation.pdf.gz | 1.5 MB | 表示 | |
XML形式データ | 9cth_validation.xml.gz | 90.9 KB | 表示 | |
CIF形式データ | 9cth_validation.cif.gz | 134.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ct/9cth ftp://data.pdbj.org/pub/pdb/validation_reports/ct/9cth | HTTPS FTP |
-関連構造データ
関連構造データ | 42405MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-Activated Factor V (FVa) ... , 2種, 2分子 AE
#1: タンパク質 | 分子量: 81274.391 Da / 分子数: 1 / 断片: Domains A1 and A2 (UNP residues 29-737) / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 組織: Blood / 参照: UniProt: P12259 |
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#2: タンパク質 | 分子量: 75283.008 Da / 分子数: 1 / 断片: Domains C1, C2, and A3 (UNP residues 1574-2224) / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 組織: Blood / 参照: UniProt: P12259 |
-Activated Factor X ... , 2種, 2分子 BC
#3: タンパク質 | 分子量: 16186.952 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: F10 / Cell (発現宿主): fibroblasts / 細胞株 (発現宿主): BHK / 発現宿主: Mesocricetus auratus (ネズミ) / 参照: UniProt: P00742 |
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#4: タンパク質 | 分子量: 26588.297 Da / 分子数: 1 / Mutation: S195A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: F10 / Cell (発現宿主): fibroblasts / 細胞株 (発現宿主): BHK / 発現宿主: Mesocricetus auratus (ネズミ) / 参照: UniProt: P00742 |
-タンパク質 / 糖 , 2種, 7分子 D
#5: タンパク質 | 分子量: 65370.113 Da / 分子数: 1 / 断片: UNP residues 44-622 / Mutation: S525A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: F2 / Cell (発現宿主): fibroblasts / 細胞株 (発現宿主): BHK / 発現宿主: Mesocricetus auratus (ネズミ) / 参照: UniProt: P00734, thrombin |
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#6: 糖 | ChemComp-NAG / |
-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Prothrombinase:Prothrombin ternary complex on lipid nanodiscs タイプ: COMPLEX 詳細: The complex is made of coagulation factor Va (derived from human plasma), active site mutated (S195A) coagulation factor Xa (Recombinantly expressed in BHK cells) and active site mutated ...詳細: The complex is made of coagulation factor Va (derived from human plasma), active site mutated (S195A) coagulation factor Xa (Recombinantly expressed in BHK cells) and active site mutated (S525A) Prothrombin (Recombinantly expressed in BHK cells). The nanodisc component of the complex is made of the scaffold protein MSP1E3D1 (Recombinantly expressed in bacteria) and the phospholipid component was Porcine Brain phosphatidylserine. Entity ID: #3-#5 / 由来: RECOMBINANT |
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分子量 | 実験値: NO |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Mesocricetus auratus (ネズミ) |
緩衝液 | pH: 7.4 / 詳細: 20 mM HEPES, 150 mM NaCl, and 5 mM CaCl2 |
試料 | 濃度: 0.01 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: Prothrombin:FVa:FXa were mixed in 2:1:2 ratio. 0.01 mg/mL total protein was used for freezing. |
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R2/2 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % |
-電子顕微鏡撮影
顕微鏡 | モデル: TFS GLACIOS |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2400 nm / 最小 デフォーカス(公称値): 800 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 電子線照射量: 51.28 e/Å2 フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 実像数: 2390 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 6.47 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 4988 / アルゴリズム: BACK PROJECTION / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 |
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拘束条件 |
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