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Serious issues with cryo-EM structures of human prothrombinase.

James A Huntington1, Alexandre Faille1, Fatma Isik Ustok1

  • 1Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Hills Road , Cambridge CB2 0XY, UK.

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|January 21, 2025
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Summary

This analysis reveals critical flaws in reported cryogenic electron microscopy structures of human prothrombinase. The study concludes the structures offer no useful information on prothrombinase complex assembly or function.

Keywords:
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Area of Science:

  • Biochemistry
  • Structural Biology
  • Hematology

Background:

  • Thrombin generation from prothrombin involves the prothrombinase enzyme complex (factor Xa and factor Va) on phospholipid membranes.
  • Recent studies reported cryogenic electron microscopy (cryo-EM) structures of human prothrombinase.

Purpose of the Study:

  • To perform a post hoc analysis of the quality of reported cryo-EM coordinates and maps.
  • To assess the validity of claimed intermolecular contacts in the prothrombinase complex structures.

Main Methods:

  • Analysis of cryo-EM data coordinates and maps from reported structures (7TPQ and 7TPP).
  • Examination of intermolecular contacts described in the original publication.

Main Results:

  • The reported cryo-EM structures are deeply flawed.
  • Not a single claimed intermolecular contact is supported by the provided maps.
  • The structures lack useful information on prothrombinase complex assembly and function.

Conclusions:

  • The two reported structures of human prothrombinase do not provide valid insights.
  • The claimed breakthrough regarding prothrombinase assembly and function is unsubstantiated.