3D69

Crystal Structure of the Fab Fragment of an Anti-Factor IX Antibody 10C12

Summary for 3D69

• Entry DOI: 10.2210/pdb3d69/pdb
• Descriptor: anti-factor IX antibody, 10C12 (2 entities in total)
• Functional Keywords: anticoagulant, 10c12, factor ix, gla domain, immune system
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 93502.44

Authors

Shi, X.L.,Huang, M.D.,Zeng, T. (deposition date: 2008-05-19, release date: 2009-03-31, Last modification date: 2024-10-16)

Primary citation

Shi, X.L.,Huang, M.D.,Zeng, T.
Crystal structure of Fab Fragment of an anti-Factor IX antibody 10C12
CHIN.J.STRUCT.CHEM., 27:995-1001, 2008

PubMed Abstract: The binding of Factor IX to membranes during blood coagulation is mediated by the N-terminal gamma-carboxyglutamic acid-rich (Gla) domain, a membrane-anchoring domain found on vitamin K-dependent blood coagulation and regulatory proteins. Conformation-specific anti-Factor IX antibodies are directed at the calcium-stabilized Gla domain and interfere with Factor IX-membrane interaction. One such antibody, 10C12, recognizes the calcium-stabilized form of the Gla domain of Factor IX. We prepared the fully carboxylated Gla domain of Factor IX by solid phase peptide synthesis and crystallized Factor IX-(1-47) in complex with Fab fragments of the 10C12 antibody. The overall structure of the Gla domain in the Factor IX-(1-47)-antibody complex at 2.2 A is similar to the structure of the Factor IX Gla domain in the presence of calcium ions as determined by NMR spectroscopy (Freedman, S. J., Furie, B. C., Furie, B., and Baleja, J. D. (1995) Biochemistry 34, 12126-12137) and by x-ray crystallography (Shikamoto, Y., Morita, T., Fujimoto, Z., and Mizuno, H. (2003) J. Biol. Chem. 278, 24090-24094). The complex structure shows that the complementarity determining region loops of the 10C12 antibody form a hydrophobic pocket to accommodate the hydrophobic patch of the Gla domain consisting of Leu-6, Phe-9, and Val-10. Polar interactions also play an important role in the antibody-antigen recognition. Furthermore, the calcium coordination network of the Factor IX Gla domain is different than in Gla domain structures of other vitamin K-dependent proteins. We conclude that this antibody is directed at the membrane binding site in the omega loop of Factor IX and blocks Factor IX function by inhibiting its interaction with membranes.

PubMed: 14722079
DOI: 10.1074/jbc.M314011200

Experimental method

X-RAY DIFFRACTION (3.77 Å)