4BXS

Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.368 
  • R-Value Work: 0.298 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis.

Lechtenberg, B.C.Murray-Rust, T.A.Johnson, D.J.Adams, T.E.Krishnaswamy, S.Camire, R.M.Huntington, J.A.

(2013) Blood 122: 2777

  • DOI: 10.1182/blood-2013-06-511733
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The prothrombinase complex, composed of the protease factor (f)Xa and cofactor fVa, efficiently converts prothrombin to thrombin by specific sequential cleavage at 2 sites. How the complex assembles and its mechanism of prothrombin processing are of ...

    The prothrombinase complex, composed of the protease factor (f)Xa and cofactor fVa, efficiently converts prothrombin to thrombin by specific sequential cleavage at 2 sites. How the complex assembles and its mechanism of prothrombin processing are of central importance to human health and disease, because insufficient thrombin generation is the root cause of hemophilia, and excessive thrombin production results in thrombosis. Efforts to determine the crystal structure of the prothrombinase complex have been thwarted by the dependence of complex formation on phospholipid membrane association. Pseutarin C is an intrinsically stable prothrombinase complex preassembled in the venom gland of the Australian Eastern Brown Snake (Pseudonaja textilis). Here we report the crystal structures of the fX-fV complex and of activated fXa from P textilis venom and the derived model of active pseutarin C. Structural analysis supports a single substrate binding channel on fVa, to which prothrombin and the intermediate meizothrombin bind in 2 different orientations, providing insight into the architecture and mechanism of the prothrombinase complex-the molecular engine of blood coagulation.


    Organizational Affiliation

    Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FACTOR X-LIKE PROTEASE
A
423Pseudonaja textilis textilisMutation(s): 0 
Find proteins for Q6IT10 (Pseudonaja textilis textilis)
Go to UniProtKB:  Q6IT10
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VENOM PROTHROMBIN ACTIVATOR PSEUTARIN-C NON-CATALYTIC SUBUNIT
V
1430Pseudonaja textilisMutation(s): 0 
Find proteins for Q7SZN0 (Pseudonaja textilis)
Go to UniProtKB:  Q7SZN0
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
V
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
V
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
V
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
V
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
CU
Query on CU

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V
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
V
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.368 
  • R-Value Work: 0.298 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 115.310α = 90.00
b = 115.310β = 90.00
c = 429.520γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Database references