7c94: Difference between revisions
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The | ==Crystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptide== | ||
<StructureSection load='7c94' size='340' side='right'caption='[[7c94]], [[Resolution|resolution]] 2.84Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7c94]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C94 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C94 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.84Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c94 OCA], [https://pdbe.org/7c94 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c94 RCSB], [https://www.ebi.ac.uk/pdbsum/7c94 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c94 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PDPN_HUMAN PDPN_HUMAN] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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 (NeuAcalpha2-3Galbetal-3 [NeuAcalpha2-6]GalNAcalphal-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 A 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. | |||
Crystal structure of an anti-podoplanin antibody bound to a disialylated O-linked glycopeptide.,Ogasawara S, Suzuki K, Naruchi K, Nakamura S, Shimabukuro J, Tsukahara N, Kaneko MK, Kato Y, Murata T Biochem Biophys Res Commun. 2020 Sep 10. pii: S0006-291X(20)31702-2. doi:, 10.1016/j.bbrc.2020.08.103. PMID:32921414<ref>PMID:32921414</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7c94" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Antibody 3D structures|Antibody 3D structures]] | ||
[[Category: | *[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]] | ||
[[Category: Nakamura | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | |||
[[Category: Mus musculus]] | |||
[[Category: Kaneko MK]] | |||
[[Category: Kato Y]] | |||
[[Category: Murata T]] | |||
[[Category: Nakamura S]] | |||
[[Category: Naruchi K]] | |||
[[Category: Ogasawara S]] | |||
[[Category: Shimabukuro J]] | |||
[[Category: Suzuki K]] | |||
[[Category: Tukahara N]] | |||
Latest revision as of 19:00, 29 November 2023
Crystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptideCrystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptide
Structural highlights
FunctionPublication Abstract from PubMedPodoplanin (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 (NeuAcalpha2-3Galbetal-3 [NeuAcalpha2-6]GalNAcalphal-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 A 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. Crystal structure of an anti-podoplanin antibody bound to a disialylated O-linked glycopeptide.,Ogasawara S, Suzuki K, Naruchi K, Nakamura S, Shimabukuro J, Tsukahara N, Kaneko MK, Kato Y, Murata T Biochem Biophys Res Commun. 2020 Sep 10. pii: S0006-291X(20)31702-2. doi:, 10.1016/j.bbrc.2020.08.103. PMID:32921414[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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