3P9W

Crystal structure of an engineered human autonomous VH Domain in complex with VEGF

Summary for 3P9W

• Entry DOI: 10.2210/pdb3p9w/pdb
• Related: 3B9V
• Descriptor: Vascular endothelial growth factor A, human VEGF (3 entities in total)
• Functional Keywords: vh, cystine knot cytokine, vegf-r, signaling protein, signaling protein-immune system complex, signaling protein/immune system
• Biological source: Homo sapiens (human); More
• Cellular location: Secreted: P15692
• Total number of polymer chains: 8
• Total formula weight: 103516.51

Authors

Ma, X.,Wiesmann, C. (deposition date: 2010-10-18, release date: 2012-04-18, Last modification date: 2024-10-16)

Primary citation

Ma, X.,Barthelemy, P.A.,Rouge, L.,Wiesmann, C.,Sidhu, S.S.
Design of Synthetic Autonomous VH Domain Libraries and Structural Analysis of a VH Domain Bound to Vascular Endothelial Growth Factor.
J.Mol.Biol., 425:2247-2259, 2013

PubMed Abstract: We compared the capacity of an autonomous heavy chain variable (VH) domain (VH-B1a) to support diversity within its antigen-binding site relative to the conventional antigen-binding fragment (Fab) from which it was derived. We find that VH-B1a can tolerate significant diversity within all three complementarity-determining regions (CDRs) and also within framework 3, and thus, VH-B1a and the Fab are similar in terms of the regions of the antigen-binding site that can tolerate diversity without compromising stability. We constructed libraries of synthetic VH domains and isolated binders with moderate affinity for vascular endothelial growth factor (VEGF) from a library in which only CDR3 was randomized. One binder was subjected to affinity maturation to derive an autonomous VH domain (VH-V1a) that recognized both human and mouse VEGF with high affinity (KD=16nM or 10nM, respectively). Structural analysis revealed that VH-V1a binds to an epitope that is distinct from the epitopes of a natural VEGF receptor and six different anti-VEGF Fabs. Moreover, VH-V1a recognizes VEGF by using an unusual paratope consisting predominantly of CDR3 but with significant contributions from framework residues within the former light chain interface. These results suggest that VH-B1a and other autonomous VH domains may be useful scaffolds to support both conventional libraries with antigen-binding sites built from the three CDR loops and, also, nonconventional libraries with antigen-binding sites built from CDR3 and the former light chain interface.

PubMed: 23507309
DOI: 10.1016/j.jmb.2013.03.020

Experimental method

X-RAY DIFFRACTION (2.41 Å)