3HXQ

Crystal Structure of Von Willebrand Factor (VWF) A1 Domain in Complex with DNA Aptamer ARC1172, an Inhibitor of VWF-Platelet Binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.694 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1.

Huang, R.H.Fremont, D.H.Diener, J.L.Schaub, R.G.Sadler, J.E.

(2009) Structure 17: 1476-1484

  • DOI: 10.1016/j.str.2009.09.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ARC1172 is a 41-mer DNA aptamer selected to bind the A1 domain of von Willebrand factor (VWF). A derivative of ARC1172 with modifications to increase intravascular survival inhibits carotid artery thrombosis in a Cynomolgus macaque model and inhibits ...

    ARC1172 is a 41-mer DNA aptamer selected to bind the A1 domain of von Willebrand factor (VWF). A derivative of ARC1172 with modifications to increase intravascular survival inhibits carotid artery thrombosis in a Cynomolgus macaque model and inhibits VWF-dependent platelet aggregation in humans, suggesting that such aptamers may be useful to prevent or treat thrombosis. In the crystal structure of a VWF A1-ARC1172 complex, the aptamer adopts a three-stem structure of mainly B-form DNA with three noncanonical base pairs and 9 unpaired residues, 6 of which are stabilized by base-base or base-deoxyribose stacking interactions. The aptamer-protein interface is characterized by cation-pi interactions involving Arg, Lys, and Gln residues, often stabilized by H-bonds with adjacent bases. The ARC1172 binding site on the A1 domain overlaps with that of botrocetin and clashes with glycoprotein Ibalpha binding at an adjacent site, which accounts for the antithrombotic activity of ARC1172 and related aptamers.


    Related Citations: 
    • First-in-human evaluation of anti von Willebrand factor therapeutic aptamer ARC1779 in healthy volunteers.
      Gilbert, J.C.,DeFeo-Fraulini, T.,Hutabarat, R.M.,Horvath, C.J.,Merlino, P.G.,Marsh, H.N.,Healy, J.M.,Boufakhreddine, S.,Holohan, T.V.,Schaub, R.G.
      (2007) Circulation 116: 2678
    • Inhibition of von Willebrand factor-mediated platelet activation and thrombosis by the anti-von Willebrand factor A1-domain aptamer ARC1779.
      Diener, J.L.,Daniel Lagasse, H.A.,Duerschmied, D.,Merhi, Y.,Tanguay, J.F.,Hutabarat, R.,Gilbert, J.,Wagner, D.D.,Schaub, R.
      (2009) J.Thromb.Haemost. 7: 1155


    Organizational Affiliation

    Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
von Willebrand Factor
A
209Homo sapiensGene Names: VWF (F8VWF)
Find proteins for P04275 (Homo sapiens)
Go to Gene View: VWF
Go to UniProtKB:  P04275
Entity ID: 2
MoleculeChainsLengthOrganism
Aptamer ARC1172B42N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.694 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 117.781α = 90.00
b = 48.512β = 90.00
c = 62.160γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-16
    Type: Atomic model
  • Version 1.3: 2012-03-21
    Type: Database references
  • Version 1.4: 2017-11-22
    Type: Database references