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7C95

Crystal structure of the anti-human podoplanin antibody Fab fragment

Summary for 7C95
Entry DOI10.2210/pdb7c95/pdb
DescriptorLight chain of Fab fragment, Heavy chain of Fab fragment, GLYCEROL, ... (6 entities in total)
Functional Keywordshuman podoplanin, monoclonal antibody, glycopeptide, immune system
Biological sourceMus musculus
More
Total number of polymer chains4
Total formula weight98563.48
Authors
Nakamura, S.,Suzuki, K.,Ogasawara, S.,Naruchi, K.,Shimabukuro, J.,Tukahara, N.,Kaneko, M.K.,Kato, Y.,Murata, T. (deposition date: 2020-06-04, release date: 2020-09-30, Last modification date: 2024-10-16)
Primary citationOgasawara, S.,Suzuki, K.,Naruchi, K.,Nakamura, S.,Shimabukuro, J.,Tsukahara, N.,Kaneko, M.K.,Kato, Y.,Murata, T.
Crystal structure of an anti-podoplanin antibody bound to a disialylated O-linked glycopeptide.
Biochem.Biophys.Res.Commun., 533:57-63, 2020
Cited by
PubMed Abstract: 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 (-LVATSVNSV-T-GIRIEDLP-) 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.
PubMed: 32921414
DOI: 10.1016/j.bbrc.2020.08.103
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.13 Å)
Structure validation

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数据于2024-11-06公开中

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