9YQ8

Cryo-EM complex of meizothrombinDESF1, factor Xa, and factor Va

Summary for 9YQ8

• Entry DOI: 10.2210/pdb9yq8/pdb
• EMDB information: 73327
• Descriptor: Coagulation factor X, Coagulation factor Va light chain, Meizothrombin, ... (5 entities in total)
• Functional Keywords: coagulation cascade, serine proteases, thrombotic, clotting factors, blood clotting
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 5
• Total formula weight: 237160.21

Authors

Stojanovski, B.M.,Mohammed, B.M.,Basore, K.,Di Cera, E. (deposition date: 2025-10-15, release date: 2026-05-20)

Primary citation

Stojanovski, B.,Mohammed, B.M.,Basore, K.,Di Cera, E.
Molecular mechanism of cleavage at R271 during prothrombin activation revealed by cryo-EM.
Blood, 2026

PubMed Abstract: The conversion of the inactive zymogen prothrombin to the active protease thrombin in the common pathway of the coagulation cascade is the molecular event responsible for the pathophysiology of hemostasis and thrombosis. The conversion entails two proteolytic cleavages at R320 and R271 by the prothrombinase complex composed of the enzyme factor Xa (fXa), the cofactor fVa, Ca2+ and phospholipids. A recent cryogenic electron microscopy (cryo-EM) structure revealed how cleavage at R320 generates the active intermediate meizothrombin in the first step of the activation pathway. Here we present the 3.8 Å resolution cryo-EM structure of a truncated form of meizothrombin (mzTDF1) bound to fVa and fXa that reveals how the second cleavage at R271 generates thrombin. The cleavage is brokered by molecular contacts that involve mostly the protease domains of mzTDF1 and fXa and largely validate the results from biochemical studies. The switch in cleavage site from R320 to R271 involves a significant reorientation rather than conformational transitions of the protease domain of mzTDF1 that moves the guanidinium group of R271 more than 20 Å into the primary specificity pocket of fXa. The findings complete the cryo-EM structural analysis of prothrombin activation along the meizothrombin pathway and advance our molecular understanding of a reaction critical to the pathophysiology of blood coagulation.

PubMed: 42008389
DOI: 10.1182/blood.2025032364

Experimental method

ELECTRON MICROSCOPY (3.84 Å)