Crystal structure of an anti-podoplanin antibody bound to a disialylated O-linked glycopeptide

Satoshi Ogasawara, Kano Suzuki, Kentaro Naruchi, Seiwa Nakamura, Junpei Shimabukuro, Nanase Tsukahara, Mika K. Kaneko, Yukinari Kato, Takeshi Murata

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1 Citation (Scopus)


Podoplanin (PDPN) is a highly O-glycosylated glycoprotein that is utilized as a specific lymphatic endothelial marker under pathophysiological conditions. We previously developed an anti-human PDPN (hPDPN) monoclonal antibody (mAb), clone LpMab-3, which recognizes the epitope, including both the peptides and the attached disialy-core-l (NeuAcα2-3Galβl-3 [NeuAcα2-6]GalNAcαl-O-Thr) structure at the Thr76 residue in hPDPN. However, it is unclear if the mAb binds directly to both the peptides and glycans. In this study, we synthesized the binding epitope region of LpMab-3 that includes the peptide (-67LVATSVNSV-T-GIRIEDLP84-) possessing a disialyl-core-1 O-glycan at Thr76, and we determined the crystal structure of the LpMab-3 Fab fragment that was bound to the synthesized glycopeptide at a 2.8 Å resolution. The six amino acid residues and two sialic acid residues are directly associated with four complementarity-determining regions (CDRs; H1, H2, H3, and L3) and four CDRs (H2, H3, L1, and L3), respectively. These results suggest that IgG is advantageous for generating binders against spacious epitopes such as glycoconjugates.

Original languageEnglish
Pages (from-to)57-63
Number of pages7
JournalBiochemical and Biophysical Research Communications
Issue number1
Publication statusPublished - 2020 Nov 26


  • Crystal structure
  • Glycopeptide
  • Monoclonal antibody
  • Podoplanin (PDPN)


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