PDBsum entry 1ijk

Blood clotting/toxin

PDB id: 1ijk

Contents

Protein chains

199 a.a. *

133 a.a. *

119 a.a. *

Waters ×94

* Residue conservation analysis

References listed in PDB file

Key reference

Title

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

Authors

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

Ref.

Structure, 2002, 10, 943-950. [DOI no: 10.1016/S0969-2126(02)00787-6]

PubMed id

12121649

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.

Figure 3.
Figure 3. Structure of the A1-Botrocetin Complex(A) Stereo view (Ca tracing) of the complex. The current model includes 199 residues from 502 to 700 of the mutant A1 domain, 133 (119) residues of the a (b) subunits of botrocetin, and 94 water molecules. There is no electron density for the loop (residues 55-60 in the b subunit). The A1 domain is in blue; the a and b subunits of botrocetin are in pink and green, respectively. Gain-of-function mutations are shown as blue balls; loss-of-function mutations are shown in red; loss of botrocetin binding mutations are shown in yellow. The I546V mutation site is shown as a green ball.(B) Space-filling model of the complex with mutation sites indicated; same view as in (A). The NMC-4 antibody (V[H]-V[L] dimer) is shown as a semitransparent molecular surface.(C) Electrostatic surface potential contoured from -15 (red) to +15 (blue) kT e^ -1. The figure was made using RASTER3D [30] and GRASP [32].

The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 943-950) copyright 2002.

Secondary reference #1

Title

Crystal structure of the von willebrand factor a1 domain and implications for the binding of platelet glycoprotein ib.

Authors

J.Emsley, M.Cruz, R.Handin, R.Liddington.

Ref.

J Biol Chem, 1998, 273, 10396-10401. [DOI no: 10.1074/jbc.273.17.10396]

PubMed id

9553097

Figure 2.
Fig. 2. Stereo C plot comparing vWF-A1 (solid lines) with vWF-A3 (dashed lines). The two molecules have been superimposed using MULTIFIT (25). The N and C termini of vWF-A1 are labeled. Every 10th residue (starting at 506) is shown as a small circle, with occasional numbering. The N- and C-proximal cysteines forming the disulfide bridge are shown as large circles.

Figure 3.
Fig. 3. Main chain schematic of the vWF-A1 domain, with -strands (arrows) and helices (coils) (drawn with MOLSCRIPT, RASTER3D, and RENDER (32-34)). The two cysteines involved the disulfide bridge are shown as yellow spheres. Sites of von Willebrand disease type IIb mutations (both natural and induced) are shown as red spheres. Mutants with reduced botrocetin binding are in green. Mutations with selective loss-of-function (reduced ristocetin-induced binding but normal botrocetin-induced binding) are in cyan (23) or black (26), and a mutant with reduced GpIb binding but normal botrocetin binding is in blue (23). The mutation of KKKK642-645 in the 5- E loop also reduces binding to heparin (26). For multiple site mutants, spheres are placed near the midpoint of the mutation.

The above figures are reproduced from the cited reference with permission from the ASBMB