Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 212.85 kDa 
• Atom Count: 11295 
• Modelled Residue Count: 1510 
• Deposited Residue Count: 1853 
• Unique protein chains: 2

4BXS

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

• PDB DOI: 10.2210/pdb4BXS/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Pseudonaja textilis
• Expression System: Escherichia coli BL21(DE3), Cricetulus griseus
• Mutation(s): No 


• Deposited: 2013-07-15 Released: 2013-07-31 
• Deposition Author(s): Lechtenberg, B.C., Murray-Rust, T.A., Johnson, D.J.D., Adams, T.E., Krishnaswamy, S., Camire, R.M., Huntington, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 0.368 
• R-Value Work: 0.298 
• R-Value Observed: 0.301 

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

• PubMed: 23869089 
• DOI: 10.1182/blood-2013-06-511733
• Primary Citation of Related Structures:  
  4BXS, 4BXW


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR X-LIKE PROTEASE	A	423	Pseudonaja textilis	Mutation(s): 0  EC: 3.4.21.6
UniProt
Find proteins for Q56VR3 (Pseudonaja textilis) Explore Q56VR3  Go to UniProtKB:  Q56VR3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VENOM PROTHROMBIN ACTIVATOR PSEUTARIN-C NON-CATALYTIC SUBUNIT	B [auth V]	1430	Pseudonaja textilis	Mutation(s): 0
UniProt
Find proteins for Q7SZN0 (Pseudonaja textilis) Explore Q7SZN0  Go to UniProtKB:  Q7SZN0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ GlyCosmos:  G80966KZ GlyGen:  G80966KZ

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth D], F [auth E]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth V]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU	J [auth V]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	H [auth V], I [auth V]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 0.368 
• R-Value Work: 0.298 
• R-Value Observed: 0.301 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.31	α = 90
b = 115.31	β = 90
c = 429.52	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-07-15 
• Released Date: 2013-07-31 
Deposition Author(s): Lechtenberg, B.C., Murray-Rust, T.A., Johnson, D.J.D., Adams, T.E., Krishnaswamy, S., Camire, R.M., Huntington, J.A.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 1.1: 2013-10-30
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary