6lz4 - Revision history

OCA at 15:05, 29 November 2023

2023-11-29T15:05:36Z

←Older revision		Revision as of 15:05, 29 November 2023
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	<StructureSection load='6lz4' size='340' side='right'caption='[[6lz4]], [[Resolution\|resolution]] 2.49Å' scene=''>		<StructureSection load='6lz4' size='340' side='right'caption='[[6lz4]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lz4]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LZ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lz4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZ4 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=6lz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lz4 OCA], [~~http~~://pdbe.org/6lz4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6lz4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6lz4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6lz4 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]] 2.49Å</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=6lz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lz4 OCA], [https://pdbe.org/6lz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lz4 RCSB], [https://www.ebi.ac.uk/pdbsum/6lz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lz4 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PDPN_MOUSE PDPN_MOUSE] Mediates effects on cell migration and adhesion through its different partners. During development plays a role in blood and lymphatic vessels separation by binding CLEC1B, triggering CLEC1B activation in platelets and leading to platelet activation and/or aggregation (PubMed:14522983, PubMed:15231832, PubMed:20110424, PubMed:17616532). Interaction with CD9, on the contrary, attenuates platelet aggregation and pulmonary metastasis induced by PDPN. Mediates effects on cell migration and adhesion through its different partners. Through MSN or EZR interaction promotes epithelial-mesenchymal transition (EMT) leading to ERZ phosphorylation and triggering RHOA activation leading to cell migration increase and invasiveness. Interaction with CD44 promotes directional cell migration in epithelial and tumor cells (By similarity). In lymph nodes (LNs), controls fibroblastic reticular cells (FRCs) adhesion to the extracellular matrix (ECM) and contraction of the actomyosin by maintaining ERM proteins (EZR; MSN and RDX) and MYL9 activation through association with unknown transmembrane proteins. Engagement of CLEC1B by PDPN promotes FRCs relaxation by blocking lateral membrane interactions leading to reduction of ERM proteins (EZR; MSN and RDX) and MYL9 activation (PubMed:25347465). Through binding with LGALS8 may participate in connection of the lymphatic endothelium to the surrounding extracellular matrix (By similarity). In keratinocytes, induces changes in cell morphology showing an elongated shape, numerous membrane protrusions, major reorganization of the actin cytoskeleton, increased motility and decreased cell adhesion (PubMed:10574709). Controls invadopodia stability and maturation leading to efficient degradation of the extracellular matrix (ECM) in tumor cells through modulation of RHOC activity in order to activate ROCK1/ROCK2 and LIMK1/LIMK2 and inactivation of CFL1 (By similarity). Required for normal lung cell proliferation and alveolus formation at birth (PubMed:12654292). Does not function as a water channel or as a regulator of aquaporin-type water channels (By similarity). Does not have any effect on folic acid or amino acid transport (PubMed:12032185).[UniProtKB:Q86YL7]<ref>PMID:10574709</ref> <ref>PMID:12032185</ref> <ref>PMID:12654292</ref> <ref>PMID:14522983</ref> <ref>PMID:15231832</ref> <ref>PMID:17616532</ref> <ref>PMID:20110424</ref> <ref>PMID:25347465</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6lz4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6lz4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Arimori, T~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Takagi, J~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Antibody fragment~~]]	+	[[Category: Arimori T]]
-	[[Category: ~~Fv-clasp]]~~	+	[[Category: Takagi J]]
-	~~[[Category: Immune system~~]]	+

OCA at 08:06, 11 November 2020

2020-11-11T08:06:53Z

←Older revision		Revision as of 08:06, 11 November 2020
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	==Crystal structure of PMab-1 Fv-clasp fragment with its antigen peptide==		==Crystal structure of PMab-1 Fv-clasp fragment with its antigen peptide==
-	<StructureSection load='6lz4' size='340' side='right'caption='[[6lz4]]' scene=''>	+	<StructureSection load='6lz4' size='340' side='right'caption='[[6lz4]], [[Resolution\|resolution]] 2.49Å' 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=6LZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LZ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lz4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LZ4 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=6lz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lz4 OCA], [http://pdbe.org/6lz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lz4 RCSB], [http://www.ebi.ac.uk/pdbsum/6lz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lz4 ProSAT]</span></td></tr>		</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=6lz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lz4 OCA], [http://pdbe.org/6lz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lz4 RCSB], [http://www.ebi.ac.uk/pdbsum/6lz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lz4 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The MAP tag system comprises a 14-residue peptide derived from mouse podoplanin and its high-affinity monoclonal antibody PMab-1. We determined the crystal structure of PMab-1 complexed with the MAP tag peptide and found that the recognition required only the N-terminal 8-residues of MAP tag sequence, enabling the shortening of the tag length without losing the affinity for PMab-1. Furthermore, the structure illustrated that the MAP tag adopts a U-shaped conformation when bound by PMab-1, suggesting that loop-inserted MAP tag would assume conformation compatible with the PMab-1 binding. We inserted the 8-residue MAP tag into multiple loop regions in various proteins including fibronectin type III domain and G protein-coupled receptors and tested if they maintain PMab-1 reactivity. Despite the conformational restraints forced by the insertion position, all MAP-inserted mutants were expressed well in mammalian cells at levels comparable to the non-tagged proteins. Furthermore, the binding by PMab-1 was fully maintained even for the mutant where MAP tag was inserted at a structurally restricted beta-hairpin, indicating that the MAP tag system has unique feature that allows placement in the middle of protein domain at desired locations. Our results indicate the versatile utility of the MAP tag system in "site-specific epitope insertion" application.
		+
		+	Site-specific epitope insertion into recombinant proteins using the MAP tag system.,Wakasa A, Kaneko MK, Kato Y, Takagi J, Arimori T J Biochem. 2020 May 9. pii: 5835287. doi: 10.1093/jb/mvaa054. PMID:32386302<ref>PMID:32386302</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6lz4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arimori T]]	+	[[Category: Arimori, T]]
-	[[Category: Takagi J]]	+	[[Category: Takagi, J]]
		+	[[Category: Antibody fragment]]
		+	[[Category: Fv-clasp]]
		+	[[Category: Immune system]]

OCA at 05:45, 20 May 2020

2020-05-20T05:45:09Z

←Older revision		Revision as of 05:45, 20 May 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6lz4 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of PMab-1 Fv-clasp fragment with its antigen peptide==
-		+	<StructureSection load='6lz4' size='340' side='right'caption='[[6lz4]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LZ4 FirstGlance]. <br>
-	~~Description~~:	+	</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=6lz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lz4 OCA], [http://pdbe.org/6lz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lz4 RCSB], [http://www.ebi.ac.uk/pdbsum/6lz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lz4 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Arimori T]]
		+	[[Category: Takagi J]]

OCA at 05:55, 11 March 2020

2020-03-11T05:55:40Z

←Older revision		Revision as of 05:55, 11 March 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6lz4 is ON HOLD	+	The entry 6lz4 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6lz4" [edit=sysop:move=sysop]

2020-02-26T08:01:26Z

Protected "6lz4" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:01, 26 February 2020

OCA: New page: '''Unreleased structure''' The entry 6lz4 is ON HOLD Authors: Description: Category: Unreleased Structures

2020-02-26T08:01:25Z

New page: '''Unreleased structure''' The entry 6lz4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6lz4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]