- PDB-9mot: Cryo-EM structure of factor Va bound to activated protein C -
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基本情報
登録情報
データベース: PDB / ID: 9mot
タイトル
Cryo-EM structure of factor Va bound to activated protein C
要素
Coagulation factor Va heavy chain
Coagulation factor Va light chain
Vitamin K-dependent protein C heavy chain
キーワード
BLOOD CLOTTING / Coagulation / Activated Factor V / Activated Protein C
機能・相同性
機能・相同性情報
activated protein C (thrombin-activated peptidase) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / response to vitamin K / platelet alpha granule / Cargo concentration in the ER / COPII-mediated vesicle transport / blood circulation / COPII-coated ER to Golgi transport vesicle / negative regulation of blood coagulation ...activated protein C (thrombin-activated peptidase) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / response to vitamin K / platelet alpha granule / Cargo concentration in the ER / COPII-mediated vesicle transport / blood circulation / COPII-coated ER to Golgi transport vesicle / negative regulation of blood coagulation / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / negative regulation of inflammatory response / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / extracellular vesicle / endoplasmic reticulum lumen / copper ion binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of apoptotic process / endoplasmic reticulum / Golgi apparatus / proteolysis / extracellular space / extracellular region / membrane / plasma membrane 類似検索 - 分子機能
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)
HL049413, HL139554 and HL147821
米国
Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital
CDI-CORE-2015-505 and CDI-CORE-2019-813
米国
The Foundation for Barnes-Jewish Hospital
3770
米国
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)
DK020579
米国
National Institutes of Health/National Cancer Institute (NIH/NCI)
CA091842
米国
引用
ジャーナル: Blood / 年: 2025 タイトル: Cryo-EM structure of coagulation factor Va bound to activated protein C. 著者: Bassem M Mohammed / Katherine Basore / Enrico Di Cera / 要旨: Coagulation factor Va (FVa) is the cofactor component of the prothrombinase complex required for rapid generation of thrombin from prothrombin in the penultimate step of the coagulation cascade. In ...Coagulation factor Va (FVa) is the cofactor component of the prothrombinase complex required for rapid generation of thrombin from prothrombin in the penultimate step of the coagulation cascade. In addition, FVa is a target for proteolytic inactivation by activated protein C (APC). Like other protein-protein interactions in the coagulation cascade, the FVa-APC interaction has long posed a challenge to structural biology and its molecular underpinnings remain unknown. A recent cryogenic electron microscopy (cryo-EM) structure of FVa has revealed the arrangement of its A1-A2-A3-C1-C2 domains and the environment of the sites of APC cleavage at R306 and R506. Here, we report the cryo-EM structure of the FVa-APC complex at 3.15 Å resolution in which the protease domain of APC engages R506 in the A2 domain of FVa through electrostatic interactions between positively charged residues in the 30-loop and 70-loop of APC and an electronegative surface of FVa. The auxiliary γ-carboxyglutamic acid and epidermal growth factor domains of APC are highly dynamic and point to solvent, without making contacts with FVa. Binding of APC displaces a large portion of the A2 domain of FVa and projects the 654VKCIPDDDEDSYEIFEP670 segment as a "latch," or exosite ligand, over the 70-loop of the enzyme. The latch induces a large conformational change of the autolysis loop of APC, which in turn promotes docking of R506 into the primary specificity pocket. The cryo-EM structure of the FVa-APC complex validates the bulk of existing biochemical data and offers molecular context for a key regulatory interaction of the coagulation cascade.
Imaging-ID: 1 / フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) / 撮影したグリッド数: 1
ID
電子線照射量 (e/Å2)
検出モード
実像数
詳細
1
51.86
COUNTING
3193
30degreestilt
2
46.6
600
3
46.89
2655
30degreestilt
4
47.19
2379
5
46.89
420
6
52.8
3210
画像スキャン
横
縦
動画フレーム数/画像
ID
Image recording-ID
Entry-ID
4096
4096
50
1
1
9MOT
4096
4096
2
2
9MOT
4096
4096
3
3
9MOT
4096
4096
4
4
9MOT
4096
4096
5
5
9MOT
4096
4096
6
6
9MOT
-
解析
EMソフトウェア
ID
名称
バージョン
カテゴリ
1
cryoSPARC
4.6.2
粒子像選択
2
EPU
画像取得
4
cryoSPARC
4.6.2
CTF補正
7
UCSF ChimeraX
1.9
モデルフィッティング
12
cryoSPARC
4.6.2
3次元再構成
13
PHENIX
1.21.2-5419
モデル精密化
14
Coot
0.9.8.95
モデル精密化
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: 3.15 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 384239 / アルゴリズム: BACK PROJECTION 詳細: 3D flex with custom mesh was used for the reconstruction クラス平均像の数: 1 / 対称性のタイプ: POINT