5xzk - Revision history

OCA at 07:28, 1 May 2024

OCA — Wed, 01 May 2024 07:28:54 GMT

←Older revision		Revision as of 07:28, 1 May 2024
Line 1:		Line 1:

	==Pholiota squarrosa lectin trimer==		==Pholiota squarrosa lectin trimer==
-	<StructureSection load='5xzk' size='340' side='right'caption='[[5xzk~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5xzk' size='340' side='right'caption='[[5xzk]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xzk]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XZK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xzk]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pholiota_squarrosa Pholiota squarrosa]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XZK 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=5xzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzk OCA], [~~http~~://pdbe.org/5xzk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xzk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xzk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzk ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=5xzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzk OCA], [https://pdbe.org/5xzk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xzk RCSB], [https://www.ebi.ac.uk/pdbsum/5xzk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzk ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A384E107_9AGAR A0A384E107_9AGAR]
-	The core alpha1-6 fucosylation-specific lectin from a mushroom Pholiota squarrosa (PhoSL) is a potential tool for precise diagnosis of cancers. This lectin consists of only 40 amino acids and can be chemically synthesized. We showed here that a synthesized PhoSL peptide formed a trimer by gel filtration and chemical cross-linking assays, and determined a structure of the PhoSL trimer by NMR. The structure possesses a beta-prism motif with a three-fold rotational symmetry, where three antiparallel beta-sheets are tightly connected by swapping of beta-strands. A triad of Trp residues comprises the structural core, forming NH-pi electrostatic interactions among the indole rings. NMR analysis with an excess amount of fucose revealed the structural basis for the molecular recognition. Namely, fucose deeply enters a pocket formed at a junction of beta-sheet edges, with the methyl group placed at the bottom. It forms a number of hydrophobic and hydrogen-bonding interactions with PhoSL residues. In spite of partial similarities to the structures of other functionally related lectins, the arrangement of the antiparallel beta-sheets in the PhoSL trimer is novel as a structural scaffold, and thus defines a novel type of lectin structure.	+
-		+
-	~~The trimeric solution structure and fucose-binding mechanism of the core fucosylation-specific lectin PhoSL.,Yamasaki K, Yamasaki T, Tateno H Sci Rep. 2018 May 17;8(1)~~:~~7740. doi: 10.1038~~/~~s41598-018-25630-2. PMID:29773815<ref>PMID:29773815<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5xzk" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Yamasaki, K~~]]	+	[[Category: Pholiota squarrosa]]
-	[[Category: ~~Fucose]]~~	+	[[Category: Yamasaki K]]
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Sugar binding protein]]~~	+
-	~~[[Category: Trimer~~]]	+

OCA at 07:01, 14 October 2020

OCA — Wed, 14 Oct 2020 07:01:47 GMT

←Older revision		Revision as of 07:01, 14 October 2020
Line 1:		Line 1:

	==Pholiota squarrosa lectin trimer==		==Pholiota squarrosa lectin trimer==
-	<StructureSection load='5xzk' size='340' side='right' caption='[[5xzk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5xzk' size='340' side='right'caption='[[5xzk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xzk]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XZK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xzk]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XZK FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5xzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzk OCA], [http://pdbe.org/5xzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xzk RCSB], [http://www.ebi.ac.uk/pdbsum/5xzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzk 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=5xzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzk OCA], [http://pdbe.org/5xzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xzk RCSB], [http://www.ebi.ac.uk/pdbsum/5xzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Yamasaki, K]]		[[Category: Yamasaki, K]]
	[[Category: Fucose]]		[[Category: Fucose]]

OCA at 05:52, 6 June 2018

OCA — Wed, 06 Jun 2018 05:52:19 GMT

←Older revision		Revision as of 05:52, 6 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xzk is ~~ON HOLD until Paper~~ Publication	+	==Pholiota squarrosa lectin trimer==
		+	<StructureSection load='5xzk' size='340' side='right' caption='[[5xzk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xzk]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XZK FirstGlance]. <br>
		+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5xzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzk OCA], [http://pdbe.org/5xzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xzk RCSB], [http://www.ebi.ac.uk/pdbsum/5xzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzk ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The core alpha1-6 fucosylation-specific lectin from a mushroom Pholiota squarrosa (PhoSL) is a potential tool for precise diagnosis of cancers. This lectin consists of only 40 amino acids and can be chemically synthesized. We showed here that a synthesized PhoSL peptide formed a trimer by gel filtration and chemical cross-linking assays, and determined a structure of the PhoSL trimer by NMR. The structure possesses a beta-prism motif with a three-fold rotational symmetry, where three antiparallel beta-sheets are tightly connected by swapping of beta-strands. A triad of Trp residues comprises the structural core, forming NH-pi electrostatic interactions among the indole rings. NMR analysis with an excess amount of fucose revealed the structural basis for the molecular recognition. Namely, fucose deeply enters a pocket formed at a junction of beta-sheet edges, with the methyl group placed at the bottom. It forms a number of hydrophobic and hydrogen-bonding interactions with PhoSL residues. In spite of partial similarities to the structures of other functionally related lectins, the arrangement of the antiparallel beta-sheets in the PhoSL trimer is novel as a structural scaffold, and thus defines a novel type of lectin structure.

-	~~Authors~~:	+	The trimeric solution structure and fucose-binding mechanism of the core fucosylation-specific lectin PhoSL.,Yamasaki K, Yamasaki T, Tateno H Sci Rep. 2018 May 17;8(1):7740. doi: 10.1038/s41598-018-25630-2. PMID:29773815<ref>PMID:29773815</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xzk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Yamasaki, K]]
		+	[[Category: Fucose]]
		+	[[Category: Lectin]]
		+	[[Category: Sugar binding protein]]
		+	[[Category: Trimer]]

OCA at 05:20, 11 October 2017

OCA — Wed, 11 Oct 2017 05:20:50 GMT

←Older revision		Revision as of 05:20, 11 October 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xzk is ON HOLD	+	The entry 5xzk is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5xzk" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 15:58:01 GMT

Protected "5xzk" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:58, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xzk is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 15:58:00 GMT

New page: '''Unreleased structure''' The entry 5xzk is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xzk is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]