7TPP

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the prothrombin-prothrombinase complex.

Ruben, E.A.Summers, B.Rau, M.J.Fitzpatrick, J.A.J.Di Cera, E.

(2022) Blood 139: 3463-3473

  • DOI: 10.1182/blood.2022015807
  • Primary Citation of Related Structures:  
    7TPP, 7TPQ

  • 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 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.


    Organizational Affiliation

    Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProthrombinA [auth E]579Homo sapiensMutation(s): 1 
Gene Names: F2
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
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Go to UniProtKB:  P00734
PHAROS:  P00734
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UniProt GroupP00734
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Factor X light chainB [auth A]139Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
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Go to UniProtKB:  P00742
PHAROS:  P00742
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UniProt GroupP00742
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VaC709Homo sapiensMutation(s): 0 
Gene Names: F5
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Find proteins for P12259 (Homo sapiens)
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PHAROS:  P12259
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UniProt GroupP12259
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VaD651Homo sapiensMutation(s): 0 
Gene Names: F5
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Find proteins for P12259 (Homo sapiens)
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PHAROS:  P12259
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UniProt GroupP12259
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Activated factor Xa heavy chainE [auth B]254Homo sapiensMutation(s): 1 
Gene Names: F10
EC: 3.4.21.6
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Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
Entity Groups  
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UniProt GroupP00742
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references