9CTH

Preliminary map of the Prothrombin-prothrombinase complex on nano discs

  • Classification: BLOOD CLOTTING
  • Organism(s): Homo sapiens
  • Expression System: Mesocricetus auratus
  • Mutation(s): Yes 

  • Deposited: 2024-07-25 Released: 2024-08-07 
  • Deposition Author(s): Stojanovski, B.M., Mohammed, B.M., Di Cera, E.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital, Foundation for Barnes-Jewish Hospital, Other private

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Prothrombin-Prothrombinase Interaction.

Stojanovski, B.M.Mohammed, B.M.Di Cera, E.

(2024) Subcell Biochem 104: 409-423

  • DOI: https://doi.org/10.1007/978-3-031-58843-3_15
  • Primary Citation of Related Structures:  
    9CTH

  • PubMed Abstract: 

    The hemostatic response to vascular injury entails a sequence of proteolytic events where several inactive zymogens of the trypsin family are converted to active proteases. The cascade starts with exposure of tissue factor from the damaged endothelium and culminates with conversion of prothrombin to thrombin in a reaction catalyzed by the prothrombinase complex composed of the enzyme factor Xa, cofactor Va, Ca 2+ , and phospholipids. This cofactor-dependent activation is paradigmatic of analogous reactions of the blood coagulation and complement cascades, which makes elucidation of its molecular mechanism of broad significance to the large class of trypsin-like zymogens to which prothrombin belongs. Because of its relevance as the most important reaction in the physiological response to vascular injury, as well as the main trigger of pathological thrombotic complications, the mechanism of prothrombin activation has been studied extensively. However, a molecular interpretation of this mechanism has become available only recently from important developments in structural biology. Here we review current knowledge on the prothrombin-prothrombinase interaction and outline future directions for the study of this key reaction of the coagulation cascade.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Activated Factor V (FVa) heavy chain709Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P12259 (Homo sapiens)
Explore P12259 
Go to UniProtKB:  P12259
PHAROS:  P12259
GTEx:  ENSG00000198734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12259
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P12259-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Activated Factor V (FVa) light chainB [auth E]651Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P12259 (Homo sapiens)
Explore P12259 
Go to UniProtKB:  P12259
PHAROS:  P12259
GTEx:  ENSG00000198734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12259
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P12259-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Activated Factor X light chainC [auth B]142Homo sapiensMutation(s): 0 
Gene Names: F10
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
GTEx:  ENSG00000126218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Activated Factor X heavy chainD [auth C]235Homo sapiensMutation(s): 1 
Gene Names: F10
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
GTEx:  ENSG00000126218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ProthrombinE [auth D]579Homo sapiensMutation(s): 1 
Gene Names: F2
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P00734-1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL049413, HL139554, HL147821
Childrens Discovery Institute of Washington University and St. Louis Childrens HospitalUnited StatesCDI-CORE-2019-813
Foundation for Barnes-Jewish HospitalUnited States3770
Other privateUnited StatesWashington University Diabetes Research Center DK020579
Other privateUnited StatesThe Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine CA091842

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Advisory