Fig. 6

The target domain of 4H11-scFv is located at the juxta-membrane upward transmembrane (TM) of MUC16. (a) Schematic representation of MUC16 structure: MUC16 can be divided by three parts: N-terminal domain (∼ 22,000 amino acid in length), tandem repeat domains interspersed with Sea urchin sperm protein Enterokinase and Agrin (SEA) domain including potential cleavage sites (DSVLV and PLARRVDR) and C-terminal domain that is further divided into an extracellular juxtamembrane portion, a single–span TM and a cytoplasmic tail of 32 amino acid length. The 4H11-scFv targets to the juxta-membrane as shown target sequence (red arrow). (b) Amino acid sequence alignment of the juxta-ectodomain among 8 different species. Secondary structure of human MUC16 is shown on the top as double β turns-linker-β-hairpin structures. Sequence alignments were made using Clustal Omega and ESPript 3.0. (c) Crystal structure and representative electron density maps of the MUC16^ecto residues (L31st -N13th) that are complexed with 4H11-scFv. The stick representation with a 2Fo-Fc electron density map for MUC16^ecto contoured at 1.0 σ shows two β- turns and one β-hairpin structures. Two β-turns (d, e) and a β-hairpin (f) structures are highlighted in the box with distances of hydrogen bonds between F28th (-N) – L31st (-O), R24th (-NH2) –T27th (-OG1), V19th (-N) – Y16th (-O) and V19th (-O) – Y16th (-N). See Table S3 for version of the detailed Phi (φ), Psi (ψ) and Omega (ω). (g) The predicted glycosylation sites in 19 residues using web-server (http://crdd.osdd.net), N-or O-glycosylation sites; ”N” (red) or “T” (blue), respectively