PDBsum entry 2adf

Blood clotting/immune system

PDB id: 2adf

Contents

Protein chains

189 a.a. *

218 a.a. *

209 a.a. *

Ligands

ACY

SO4 ×2

GOL

Waters ×442

* Residue conservation analysis

PDB id:

2adf

Name:

Blood clotting/immune system

Title:

Crystal structure and paratope determination of 82d6a3, an antithrombotic antibody directed against the von willebrand factor a3-domain

Structure:

Von willebrand factor. Chain: a. Fragment: a3 domain. Synonym: vwf. Engineered: yes. 82d6a3 igg. Chain: h. Fragment: fab. 82d6a3 igg.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Mus musculus. House mouse. Organism_taxid: 10090. Secretion: ascites.

Biol. unit:

Trimer (from PQS)

Resolution:

1.90Å R-factor: 0.192 R-free: 0.220

Authors:

S.Staelens,M.A.Hadders,S.Vauterin,C.Platteau,K.Vanhoorelbeke, E.G.Huizinga,H.Deckmyn

Key ref:

S.Staelens et al. (2006). Paratope determination of the antithrombotic antibody 82D6A3 based on the crystal structure of its complex with the von Willebrand factor A3-domain. J Biol Chem, 281, 2225-2231. PubMed id: 16314412 DOI: 10.1074/jbc.M508191200

Date:

20-Jul-05 Release date: 06-Dec-05

Protein chain

P04275  (VWF_HUMAN) -  von Willebrand factor from Homo sapiens

Seq: 2813 a.a.

Struc: 189 a.a.

Protein chain

P84751  (HVM63_MOUSE) -  Ig heavy chain Mem5 (Fragment) from Mus musculus

Seq: 237 a.a.

Struc: 218 a.a.*

Protein chain

No UniProt id for this chain

Struc: 209 a.a.

* PDB and UniProt seqs differ at 60 residue positions (black crosses)

DOI no: 10.1074/jbc.M508191200

J Biol Chem 281:2225-2231 (2006)

PubMed id: 16314412

Paratope determination of the antithrombotic antibody 82D6A3 based on the crystal structure of its complex with the von Willebrand factor A3-domain.

S.Staelens, M.A.Hadders, S.Vauterin, C.Platteau, M.De Maeyer, K.Vanhoorelbeke, E.G.Huizinga, H.Deckmyn.

ABSTRACT

The antithrombotic monoclonal antibody 82D6A3 is directed against amino acids Arg-963, Pro-981, Asp-1009, Arg-1016, Ser-1020, Met-1022, and His-1023 of the von Willebrand factor A3-domain (Vanhoorelbeke, K., Depraetere, H., Romijn, R. A., Huizinga, E., De Maeyer, M., and Deckmyn, H. (2003) J. Biol. Chem. 278, 37815-37821). By this, it potently inhibits the interaction of von Willebrand factor to collagens, which is a prerequisite for blood platelet adhesion to the injured vessel wall at sites of high shear. To fully understand the mode of action of 82D6A3 at the molecular level, we resolved its crystal structure in complex with the A3-domain and fine mapped its paratope by construction and characterization of 13 mutants. The paratope predominantly consists of two short sequences in the heavy chain CDR1 (Asn-31 and Tyr-32) and CDR3 (Asp-99, Pro-101, Tyr-102 and Tyr-103), forming one patch on the surface of the antibody. Trp-50 of the heavy and His-49 of the light chain, both situated adjacent to the patch, play ancillary roles in antigen binding. The crystal structure furthermore confirms the epitope location, which largely overlaps with the collagen binding site deduced from mutagenesis of the A3-domain (Romijn, R. A., Westein, E., Bouma, B., Schiphorst, M. E., Sixma, J. J., Lenting, P. J., and Huizinga, E. G. (2003) J. Biol. Chem. 278, 15035-15039). We herewith further consolidate the location of the collagen binding site and reveal that the potent action of the antibody is due to direct competition for the same interaction site. This information allows the design of a paratope-mimicking peptide with antithrombotic properties.

Selected figure(s)

Figure 2.
FIGURE 2. Interactions between 82D6A3 and the VWF A3-domain. Close-up views of CDRs and interacting regions of the A3-domain. Residues that have intermolecular contacts closer than 4 Å are depicted in stick representation. Hydrogen bonds and salt bridges are shown as dashed lines. Coloring of ribbons and loops is identical to Fig. 1A.

Figure 5.
FIGURE 5. The paratope of 82D6A3. A, ribbon diagram of the variable domains of 82D6A3 with amino acids of the paratope shown in stick representation and colored according to the extent of residual VWF binding observed if mutated to alanine: 0–40%, red; 40–80%, yellow; 80–100%, green. B, surface representation of the variable domains of 82D6A3 with surfaces corresponding to residues in the paratope color coded as in panel A.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 2225-2231) copyright 2006.

Figures were selected by an automated process.