Serious issues with cryo-EM structures of human prothrombinase
Thrombin is generated from prothrombin through sequential cleavage at two sites by the enzyme complex prothrombinase, composed of a serine protease, factor (f) Xa and a cofactor, fVa, on phospholipid membranes. In a recent paper published in Blood, Ruben et al. (Ruben et al. 2022 Blood 139, 3463–347...
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The Royal Society
2025-01-01
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| Online Access: | https://royalsocietypublishing.org/doi/10.1098/rsob.240193 |
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| author | James A. Huntington Alexandre Faille Fatma Isik Ustok |
| author_facet | James A. Huntington Alexandre Faille Fatma Isik Ustok |
| author_sort | James A. Huntington |
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| description | Thrombin is generated from prothrombin through sequential cleavage at two sites by the enzyme complex prothrombinase, composed of a serine protease, factor (f) Xa and a cofactor, fVa, on phospholipid membranes. In a recent paper published in Blood, Ruben et al. (Ruben et al. 2022 Blood 139, 3463–3473 (doi:10.1182/blood.2022015807)) reported a major breakthrough in the field: the cryogenic electron microscopy structures of human prothrombinase on nanodiscs at 5.5 Å resolution (7TPQ) and of a catalytically inert human prothrombinase with its substrate prothrombin in the absence of any membrane at 4.1 Å resolution (7TPP). As is the norm in structural biology, the original paper was reviewed without access to the coordinates and maps, and it was therefore not possible for referees to assess the validity of the structures or their interpretations. In this article, we provide a post hoc analysis of the quality of the reported coordinates and maps, and look closely at the claimed intermolecular contacts on which the supposed breakthrough depends. We demonstrate that the work is deeply flawed, with not a single claimed intermolecular contact supported by the map, and conclude that the two reported structures do not contain any useful information regarding the assembly or function of the prothrombinase complex. |
| format | Article |
| id | doaj-art-2b03e4190f214fc68a68dba9dc8ed06f |
| institution | Kabale University |
| issn | 2046-2441 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | The Royal Society |
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| series | Open Biology |
| spelling | doaj-art-2b03e4190f214fc68a68dba9dc8ed06f2025-01-22T00:07:47ZengThe Royal SocietyOpen Biology2046-24412025-01-0115110.1098/rsob.240193Serious issues with cryo-EM structures of human prothrombinaseJames A. Huntington0Alexandre Faille1Fatma Isik Ustok2Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Hills Road , Cambridge CB2 0XY, UKDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Hills Road , Cambridge CB2 0XY, UKDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Hills Road , Cambridge CB2 0XY, UKThrombin is generated from prothrombin through sequential cleavage at two sites by the enzyme complex prothrombinase, composed of a serine protease, factor (f) Xa and a cofactor, fVa, on phospholipid membranes. In a recent paper published in Blood, Ruben et al. (Ruben et al. 2022 Blood 139, 3463–3473 (doi:10.1182/blood.2022015807)) reported a major breakthrough in the field: the cryogenic electron microscopy structures of human prothrombinase on nanodiscs at 5.5 Å resolution (7TPQ) and of a catalytically inert human prothrombinase with its substrate prothrombin in the absence of any membrane at 4.1 Å resolution (7TPP). As is the norm in structural biology, the original paper was reviewed without access to the coordinates and maps, and it was therefore not possible for referees to assess the validity of the structures or their interpretations. In this article, we provide a post hoc analysis of the quality of the reported coordinates and maps, and look closely at the claimed intermolecular contacts on which the supposed breakthrough depends. We demonstrate that the work is deeply flawed, with not a single claimed intermolecular contact supported by the map, and conclude that the two reported structures do not contain any useful information regarding the assembly or function of the prothrombinase complex.https://royalsocietypublishing.org/doi/10.1098/rsob.240193bloodcryo-EMhaemostasis |
| spellingShingle | James A. Huntington Alexandre Faille Fatma Isik Ustok Serious issues with cryo-EM structures of human prothrombinase Open Biology blood cryo-EM haemostasis |
| title | Serious issues with cryo-EM structures of human prothrombinase |
| title_full | Serious issues with cryo-EM structures of human prothrombinase |
| title_fullStr | Serious issues with cryo-EM structures of human prothrombinase |
| title_full_unstemmed | Serious issues with cryo-EM structures of human prothrombinase |
| title_short | Serious issues with cryo-EM structures of human prothrombinase |
| title_sort | serious issues with cryo em structures of human prothrombinase |
| topic | blood cryo-EM haemostasis |
| url | https://royalsocietypublishing.org/doi/10.1098/rsob.240193 |
| work_keys_str_mv | AT jamesahuntington seriousissueswithcryoemstructuresofhumanprothrombinase AT alexandrefaille seriousissueswithcryoemstructuresofhumanprothrombinase AT fatmaisikustok seriousissueswithcryoemstructuresofhumanprothrombinase |