Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53.41 kDa 
• Atom Count: 3760 
• Residue Count: 451 
• Unique protein chains: 3

1IJK

The von Willebrand Factor mutant (I546V) A1 domain-botrocetin Complex

• DOI: 10.2210/pdb1IJK/pdb

• Classification: BLOOD CLOTTING/TOXIN
• Organism(s): Homo sapiens, Bothrops jararaca
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-04-26 Released: 2002-07-10 
• Deposition Author(s): Fukuda, K., Doggett, T.A., Bankston, L.A., Cruz, M.A., Diacovo, T.G., Liddington, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.279 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 

Literature

Structural basis of von Willebrand factor activation by the snake toxin botrocetin.

Fukuda, K., Doggett, T.A., Bankston, L.A., Cruz, M.A., Diacovo, T.G., Liddington, R.C.

(2002) Structure 10: 943-950

• PubMed: 12121649 
• DOI: 10.1016/s0969-2126(02)00787-6
• Primary Citation of Related Structures:  
  1IJB, 1IJK


• PubMed Abstract: 
  

The A1 domain of von Willebrand factor (vWF) mediates platelet adhesion to sites of vascular injury by binding to the platelet receptor glycoprotein Ib (GpIb), an interaction that is regulated by hydrodynamic shear forces. The GpIb binding surface of A1 is distinct from a regulatory region, suggesting that ligand binding is controlled allosterically. Here we report the crystal structures of the "gain-of-function" mutant A1 domain (I546V) and its complex with the exogenous activator botrocetin. We show that botrocetin switches the mutant A1 back toward the wild-type conformation, suggesting that affinity is enhanced by augmenting the GpIb binding surface rather than through allosteric control. Functional studies of platelet adhesion under flow further suggest that the activation mechanism is distinct from that of the gain-of-function mutation.

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Related Citations: 

• Crystal structure of the von Willebrand factor A1 domain and implications for the binding of platelet glycoprotein Ib
  Emsley, J., Cruz, M., Handin, R., Liddington, R.
  (1998) J Biol Chem 273: 10396

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Organizational Affiliation: 

The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Willebrand factor	A	202	Homo sapiens	Mutation(s): 1  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	Sequence Length	Organism	Details	Image
Botrocetin	B	133	Bothrops jararaca	Mutation(s): 0
Find proteins for P22029 (Bothrops jararaca) Explore P22029  Go to UniProtKB:  P22029

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Botrocetin	C	125	Bothrops jararaca	Mutation(s): 0
Find proteins for P22030 (Bothrops jararaca) Explore P22030  Go to UniProtKB:  P22030

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.279 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.664	α = 90
b = 66.672	β = 105.41
c = 69.402	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-04-26 
• Released Date: 2002-07-10 
Deposition Author(s): Fukuda, K., Doggett, T.A., Bankston, L.A., Cruz, M.A., Diacovo, T.G., Liddington, R.C.

Revision History 

• Version 1.0: 2002-07-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance