PDBsum entry 1fns

Immune system

PDB id: 1fns

Contents

Protein chains

214 a.a. *

220 a.a. *

196 a.a. *

Waters ×636

* Residue conservation analysis

PDB id:

1fns

Name:

Immune system

Title:

Crystal structure of the von willebrand factor (vwf) a1 domain i546v mutant in complex with the function blocking fab nmc4

Structure:

Immunoglobulin nmc-4 igg1. Chain: l. Fragment: fab fragment, light chain. Immunoglobulin nmc-4 igg1. Chain: h. Fragment: fab fragment, heavy chain. Von willebrand factor. Chain: a. Fragment: a1 domain residues 507 - 702, or glycoprotein iba

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Cell: hybridoma cells, mopc21 cells. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.00Å R-factor: 0.172 R-free: 0.207

Authors:

K.I.Varughese

Key ref:

R.Celikel et al. (2000). von Willebrand factor conformation and adhesive function is modulated by an internalized water molecule. Nat Struct Biol, 7, 881-884. PubMed id: 11017197 DOI: 10.1038/79639

Date:

23-Aug-00 Release date: 18-Oct-00

Protein chain

P01837  (IGKC_MOUSE) -  Immunoglobulin kappa constant from Mus musculus

Seq: 107 a.a.

Struc: 214 a.a.

Protein chain

P01868  (IGHG1_MOUSE) -  Ig gamma-1 chain C region secreted form from Mus musculus

Seq: 324 a.a.

Struc: 220 a.a.*

Protein chain

P04275  (VWF_HUMAN) -  von Willebrand factor from Homo sapiens

Seq: 2813 a.a.

Struc: 196 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DOI no: 10.1038/79639

Nat Struct Biol 7:881-884 (2000)

PubMed id: 11017197

von Willebrand factor conformation and adhesive function is modulated by an internalized water molecule.

R.Celikel, Z.M.Ruggeri, K.I.Varughese.

ABSTRACT

Platelet participation in hemostasis and arterial thrombosis requires the binding of glycoprotein (GP) Ibalpha to von Willebrand factor (vWF). Hemodynamic forces enhance this interaction, an effect mimicked by the substitution I546V in the vWF A1 domain. A water molecule becomes internalized near the deleted Ile methyl group. The change in hydrophobicity of the local environment causes positional changes propagated over a distance of 27 A. As a consequence, a major reorientation of a peptide plane occurs in a surface loop involved in GP Ibalpha binding. This distinct vWF conformation shows increased platelet adhesion and provides a structural model for the initial regulation of thrombus formation.

Selected figure(s)

Figure 1.
Figure 1. Location of the I546V mutation and its effects on platelet adhesion. a, Stereo view of the vWF A1 domain presented as a ribbon structure, with -strands in yellow and -helices in purple connected by loops. Note the position of the side chain of Ile 546. The loops preceding and following strand 3, site of the major conformational changes caused by the I546V substitution, are colored in green. The figure was produced with Bobscript^28. b, Velocity of platelets rolling on wild-type or I546V mutant vWF A1 domain in a flow field with wall shear rate of 1500 s^ -1. Results are presented as number of platelets within defined velocity categories. Platelets rolling on the mutant A1 domain had a median velocity of 4.2 m s^-1 compared to 44.7 m s^ -1 on the wild type control. A video clip showing the real time interaction of flowing platelets with wild type and mutant A1 domain is provided as supplementary material.

Figure 4.
Figure 4. Platelet adhesion to mutant vWF A1 domain fragments. Amino acid substitutions are indicated with the one letter code of the native and mutant residues. Single substitutions with Ala caused essentially complete loss of function at the following positions: Glu 557 in strand 2; His 559 in loop 2- 3; Tyr 565 in strand 3; Lys 572 in loop 3- 2; Glu 596 and Lys 599 in helix 3. The G561S substitution in the 2- 3 loop impaired the function of the wild type A1 domain as well as of the I546V mutant. In contrast, control mutations of Lys 585 in loop 2- 3, Arg 632 in helix 4, Lys 644 in loop 4- 5, and His 656 in loop 5- 5 had minimal or no effect on function. The number of surface interacting platelets was counted between 1 and 4 min from the beginning of flow; the wall shear rate was 1,500 s^-1. The results of mutant fragments are expressed as a percentage of those obtained with a wild type control tested on the same experimental day. The average number of platelets interacting with wild type vWF fragment was 57 (n = 11). The results represent the mean with standard error of the mean of two to four separate experiments performed with each mutant fragment.
Video clips can be viewed on the following web sites:http://www.scripps.edu/mem/biochem/KI and http://www.scripps.edu/mem/eht/ruggeri. These clips show the rolling of platelets, seen as white round objects, tethered to immobilized wild type A1 domain (top half of the screen) or I546V mutant A1 domain (lower half of the screen). The wall shear rate was 1500 s^ -1. Platelets interacting with the mutant A1 domain roll with considerably lower velocity (median = 4.2 m s^-1) than those interacting with the wild type control (median = 44.7 m s^ -1). The few larger objects that appear transiently in both screens and move rapidly are leukocytes that interact briefly with activated platelets on the surface.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 881-884) copyright 2000.

Figures were selected by an automated process.