5K64

Crystal structure of VEGF binding IgG1-Fc (Fcab 448)

Summary for 5K64

• Entry DOI: 10.2210/pdb5k64/pdb
• Descriptor: Ig gamma-1 chain C region, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (6 entities in total)
• Functional Keywords: immune system, antibody engineering, immunoglobulin g1, fc fragment, glycosylations, ch3 domain, fcab, vegf, vascular endothelial growth factor
• Biological source: Homo sapiens (Human)
• Cellular location: Secreted : P01857
• Total number of polymer chains: 2
• Total formula weight: 53943.01

Authors

Humm, A.,Lobner, E.,Kitzmuller, M.,Mlynek, G.,Obinger, C.,Djinovic-Carugo, K. (deposition date: 2016-05-24, release date: 2017-09-06, Last modification date: 2024-11-13)

Primary citation

Lobner, E.,Humm, A.S.,Mlynek, G.,Kubinger, K.,Kitzmuller, M.,Traxlmayr, M.W.,Djinovic-Carugo, K.,Obinger, C.
Two-faced Fcab prevents polymerization with VEGF and reveals thermodynamics and the 2.15 angstrom crystal structure of the complex.
MAbs, 9:1088-1104, 2017

PubMed Abstract: Fcabs (Fc domain with antigen-binding sites) are promising novel therapeutics. By engineering of the C-terminal loops of the CH3 domains, 2 antigen binding sites can be inserted in close proximity. To elucidate the binding mode(s) between homodimeric Fcabs and small homodimeric antigens, the interaction between the Fcabs 448 and CT6 (having the AB, CD and EF loops and the C-termini engineered) with homodimeric VEGF was investigated. The crystal structures of these Fcabs, which form polymers with the antigen VEGF in solution, were determined. However, construction of heterodimeric Fcabs (JanusFcabs: one chain Fc-wt, one chain VEGF-binding) results in formation of distinct JanusFcab-VEGF complexes (2:1), which allowed elucidation of the crystal structure of the JanusCT6-VEGF complex at 2.15 Å resolution. VEGF binding to Janus448 and JanusCT6 is shown to be entropically unfavorable, but enthalpically favorable. Structure-function relationships are discussed with respect to Fcab design and engineering strategies.

PubMed: 28816592
DOI: 10.1080/19420862.2017.1364825

Experimental method

X-RAY DIFFRACTION (2.44 Å)