7TPP

Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom resolution

7TPP の概要

• エントリーDOI: 10.2210/pdb7tpp/pdb
• EMDBエントリー: 26060
• 分子名称: Prothrombin, Factor X light chain, Coagulation factor Va, ... (5 entities in total)
• 機能のキーワード: prothrombin prothrombinase, blood clotting
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 5
• 化学式量合計: 266205.49

構造登録者

Di Cera, E.,Ruben, E.A. (登録日: 2022-01-25, 公開日: 2022-05-04, 最終更新日: 2024-10-09)

主引用文献

Ruben, E.A.,Summers, B.,Rau, M.J.,Fitzpatrick, J.A.J.,Di Cera, E.
Cryo-EM structure of the prothrombin-prothrombinase complex.
Blood, 139:3463-3473, 2022

PubMed Abstract: The intrinsic and extrinsic pathways of the coagulation cascade converge to a common step where the prothrombinase complex, comprising the enzyme factor Xa (fXa), the cofactor fVa, Ca2+ and phospholipids, activates the zymogen prothrombin to the protease thrombin. The reaction entails cleavage at 2 sites, R271 and R320, generating the intermediates prethrombin 2 and meizothrombin, respectively. The molecular basis of these interactions that are central to hemostasis remains elusive. We solved 2 cryogenic electron microscopy (cryo-EM) structures of the fVa-fXa complex, 1 free on nanodiscs at 5.3-Å resolution and the other bound to prothrombin at near atomic 4.1-Å resolution. In the prothrombin-fVa-fXa complex, the Gla domains of fXa and prothrombin align on a plane with the C1 and C2 domains of fVa for interaction with membranes. Prothrombin and fXa emerge from this plane in curved conformations that bring their protease domains in contact with each other against the A2 domain of fVa. The 672ESTVMATRKMHDRLEPEDEE691 segment of the A2 domain closes on the protease domain of fXa like a lid to fix orientation of the active site. The 696YDYQNRL702 segment binds to prothrombin and establishes the pathway of activation by sequestering R271 against D697 and directing R320 toward the active site of fXa. The cryo-EM structure provides a molecular view of prothrombin activation along the meizothrombin pathway and suggests a mechanism for cleavage at the alternative R271 site. The findings advance our basic knowledge of a key step of coagulation and bear broad relevance to other interactions in the blood.

PubMed: 35427420
DOI: 10.1182/blood.2022015807

実験手法

ELECTRON MICROSCOPY (4.1 Å)