Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 36.77 kDa 
• Atom Count: 2559 
• Residue Count: 242 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3HXQ

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

• DOI: 10.2210/pdb3HXQ/pdb
• NDB: NA0064

• Classification: BLOOD CLOTTING/BLOOD CLOTTING REGULATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-21 Released: 2009-11-17 
• Deposition Author(s): Huang, R.H., Sadler, J.E., Fremont, D.H., Diener, J.L., Schaub, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.279 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

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

• PubMed: 19913482 
• DOI: 10.1016/j.str.2009.09.011
• Primary Citation of Related Structures:  
  3HXO, 3HXQ


• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Willebrand Factor	A	209	Homo sapiens	Mutation(s): 0  Gene Names: VWF, F8VWF
Find proteins for P04275 (Homo sapiens) Explore P04275  Go to UniProtKB:  P04275
NIH Common Fund Data Resources
PHAROS:  P04275 GTEx:  ENSG00000110799

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Aptamer ARC1172	B	42	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.279 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.781	α = 90
b = 48.512	β = 90
c = 62.16	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-21 
• Released Date: 2009-11-17 
Deposition Author(s): Huang, R.H., Sadler, J.E., Fremont, D.H., Diener, J.L., Schaub, R.G.

Revision History 

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