7c95 - Revision history

OCA at 16:00, 29 November 2023

OCA — Wed, 29 Nov 2023 16:00:43 GMT

←Older revision		Revision as of 16:00, 29 November 2023
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-	====	+	==Crystal structure of the anti-human podoplanin antibody Fab fragment==
-	<StructureSection load='7c95' size='340' side='right'caption='[[7c95]]' scene=''>	+	<StructureSection load='7c95' size='340' side='right'caption='[[7c95]], [[Resolution\|resolution]] 2.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7c95]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C95 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C95 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7c95 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c95 OCA], [~~http~~://pdbe.org/7c95 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7c95 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7c95 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7c95 ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.13Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7c95 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c95 OCA], [https://pdbe.org/7c95 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c95 RCSB], [https://www.ebi.ac.uk/pdbsum/7c95 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c95 ProSAT]</span></td></tr>
	</table>		</table>
		+	<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>
		+	</div>
		+	<div class="pdbe-citations 7c95" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[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]]

OCA at 07:14, 30 September 2020

OCA — Wed, 30 Sep 2020 07:14:37 GMT

←Older revision		Revision as of 07:14, 30 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7c95 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7c95' size='340' side='right'caption='[[7c95]]' scene=''>
-	~~Authors~~: ~~Nakamura, S~~.~~, Suzuki, K~~.~~, Ogasawara, S~~.~~, Naruchi, K~~.~~, Shimabukuro, J~~.~~, Tukahara, N~~.~~, Kaneko, M.K., Kato, Y., Murata, T~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of Fab2~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7c95 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c95 OCA], [http://pdbe.org/7c95 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7c95 RCSB], [http://www.ebi.ac.uk/pdbsum/7c95 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7c95 ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Murata~~, ~~T]]~~	+	__TOC__
-	[~~[Category~~: ~~Kaneko, M~~.K]]	+	</StructureSection>
-	[[~~Category~~: ~~Nakamura, S~~]]	+	[[Category: Large Structures]]
-	~~[[Category: Suzuki~~, ~~K]]~~	+	[[Category: Z-disk]]
-	[~~[Category~~: ~~Naruchi, K~~]]	+
-	~~[[Category: Kato~~, ~~Y]]~~	+
-	[~~[Category~~: ~~Ogasawara, S]~~]	+
-	[[Category: ~~Shimabukuro, J~~]]	+
-	[[Category: ~~Tukahara, N~~]]	+

OCA at 18:50, 24 June 2020

OCA — Wed, 24 Jun 2020 18:50:29 GMT

←Older revision		Revision as of 18:50, 24 June 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7c95 is ON HOLD	+	The entry 7c95 is ON HOLD until Paper Publication

	Authors: Nakamura, S., Suzuki, K., Ogasawara, S., Naruchi, K., Shimabukuro, J., Tukahara, N., Kaneko, M.K., Kato, Y., Murata, T.		Authors: Nakamura, S., Suzuki, K., Ogasawara, S., Naruchi, K., Shimabukuro, J., Tukahara, N., Kaneko, M.K., Kato, Y., Murata, T.
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	Description: Crystal structure of Fab2		Description: Crystal structure of Fab2
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kato, Y]]
	[[Category: Murata, T]]		[[Category: Murata, T]]
-	[[Category: Ogasawara, S]]
-	[[Category: Shimabukuro, J]]
	[[Category: Kaneko, M.K]]		[[Category: Kaneko, M.K]]
	[[Category: Nakamura, S]]		[[Category: Nakamura, S]]
	[[Category: Suzuki, K]]		[[Category: Suzuki, K]]
-	[[Category: Tukahara, N]]
	[[Category: Naruchi, K]]		[[Category: Naruchi, K]]
		+	[[Category: Kato, Y]]
		+	[[Category: Ogasawara, S]]
		+	[[Category: Shimabukuro, J]]
		+	[[Category: Tukahara, N]]

OCA: Protected "7c95" [edit=sysop:move=sysop]

OCA — Wed, 10 Jun 2020 05:20:05 GMT

Protected "7c95" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:20, 10 June 2020

OCA: New page: '''Unreleased structure''' The entry 7c95 is ON HOLD Authors: Nakamura, S., Suzuki, K., Ogasawara, S., Naruchi, K., Shimabukuro, J., Tukahara, N., Kaneko, M.K., Kato, Y., Murata, T. De...

OCA — Wed, 10 Jun 2020 05:20:04 GMT

New page: '''Unreleased structure''' The entry 7c95 is ON HOLD Authors: Nakamura, S., Suzuki, K., Ogasawara, S., Naruchi, K., Shimabukuro, J., Tukahara, N., Kaneko, M.K., Kato, Y., Murata, T. De...

New page

'''Unreleased structure'''

The entry 7c95 is ON HOLD

Authors: Nakamura, S., Suzuki, K., Ogasawara, S., Naruchi, K., Shimabukuro, J., Tukahara, N., Kaneko, M.K., Kato, Y., Murata, T.

Description: Crystal structure of Fab2
[[Category: Unreleased Structures]]
[[Category: Kato, Y]]
[[Category: Murata, T]]
[[Category: Ogasawara, S]]
[[Category: Shimabukuro, J]]
[[Category: Kaneko, M.K]]
[[Category: Nakamura, S]]
[[Category: Suzuki, K]]
[[Category: Tukahara, N]]
[[Category: Naruchi, K]]