4BXW | pdb_00004bxw

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

PDB DOI: https://doi.org/10.2210/pdb4BXW/pdb

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

Deposited: 2013-07-16 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free:
0.233 (Depositor), 0.216 (DCC)
R-Value Work:
0.155 (Depositor), 0.156 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1182/blood-2013-06-511733
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 97.23 kDa
Atom Count: 4,538
Modeled Residue Count: 581
Deposited Residue Count: 864
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR XA	A, B	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q56VR3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR V	C [auth F]	18	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for Q593B6 (Pseudonaja textilis) Explore Q593B6 Go to UniProtKB: Q593B6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q593B6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0GJ Query on 0GJ Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide C₁₄ H₂₈ Cl N₆ O₅ XELWNHKFCNMWQO-LPEHRKFASA-O		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000288 (0GJ) Query on PRD_000288	D [auth A], G [auth B]	GLU-GLY-ARG-CHLOROMETHYL KETONE	Peptide-like / Inhibitor		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.233 (Depositor), 0.216 (DCC)
R-Value Work: 0.155 (Depositor), 0.156 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.31	α = 90
b = 179.31	β = 90
c = 179.31	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-31
Type: Initial release
Version 1.1: 2013-10-30
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary