5gzg - Revision history

OCA at 09:14, 20 March 2024

2024-03-20T09:14:18Z

←Older revision		Revision as of 09:14, 20 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/LEG8_HUMAN LEG8_HUMAN] Lectin with a marked preference for 3'-O-sialylated and 3'-O-sulfated glycans.<ref>PMID:21288902</ref>		[https://www.uniprot.org/uniprot/LEG8_HUMAN LEG8_HUMAN] Lectin with a marked preference for 3'-O-sialylated and 3'-O-sulfated glycans.<ref>PMID:21288902</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Galectin-8 (Gal-8) plays a significant role in normal immunological function as well as in cancer. This lectin contains two carbohydrate recognition domains (CRD) connected by a peptide linker. The N-terminal CRD determines ligand binding specificity, whereas the linker has been proposed to regulate overall Gal-8 function, including multimerization and biological activity. Here, we crystallized the Gal-8 N-terminal CRD with the peptide linker using a crystallization condition that contains Ni(2+). The Ni(2+) ion was found to be complexed between two CRDs via crystal packing contacts. The coordination between Ni(2+) and Asp25 plays an indirect role in determining the structure of beta-strand F0 and in influencing the linker conformation which could not be defined due to its dynamic nature. The linker was also shortened in situ and crystallized under a different condition, leading to a higher resolution structure refined to 1.08 A. This crystal structure allowed definition of a short portion of the linker interacting with the Gal-8 N-terminal tail via ionic interactions and hydrogen bonds. Observation of two Gal-8 N-terminal CRD structures implies that the N-terminal tail and the linker may influence each other's conformation. In addition, under specific crystallization conditions, glycerol could replace lactose and was observed at the carbohydrate binding site. However, glycerol did not show inhibition activity in hemagglutination assay.
-
-	Crystallization of Galectin-8 Linker Reveals Intricate Relationship between the N-terminal Tail and the Linker.,Si Y, Wang Y, Gao J, Song C, Feng S, Zhou Y, Tai G, Su J Int J Mol Sci. 2016 Dec 12;17(12). pii: ijms17122088. doi: 10.3390/ijms17122088. PMID:27973456<ref>PMID:27973456</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5gzg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 11:46, 2 August 2023

2023-08-02T11:46:50Z

←Older revision		Revision as of 11:46, 2 August 2023
Line 3:		Line 3:
	<StructureSection load='5gzg' size='340' side='right'caption='[[5gzg]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5gzg' size='340' side='right'caption='[[5gzg]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gzg]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GZG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GZG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gzg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GZG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GZG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=LAT:BETA~~-~~LACTOSE'>LAT</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>~~</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]] 1.997Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5gzc\|5gzc]], [[5gzd\|5gzd]], [[5gze\|5gze]], [[5gzf\|5gzf]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PRD_900004:beta-lactose'>PRD_900004</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class~~=~~"sblockDat">LGALS8 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~</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=5gzg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gzg OCA], [https://pdbe.org/5gzg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gzg RCSB], [https://www.ebi.ac.uk/pdbsum/5gzg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gzg ProSAT]</span></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=5gzg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gzg OCA], [~~http~~://pdbe.org/5gzg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gzg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gzg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gzg ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LEG8_HUMAN LEG8_HUMAN]] Lectin with a marked preference for 3'-O-sialylated and 3'-O-sulfated glycans.<ref>PMID:21288902</ref>	+	[https://www.uniprot.org/uniprot/LEG8_HUMAN LEG8_HUMAN] Lectin with a marked preference for 3'-O-sialylated and 3'-O-sulfated glycans.<ref>PMID:21288902</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Si~~, Y L~~]]	+	[[Category: Si YL]]
-	[[Category: Su~~, J Y]]~~	+	[[Category: Su JY]]
-	~~[[Category: Galectin-8 n-terminal domain carbohydrate recognition domain]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 11:39, 25 December 2019

2019-12-25T11:39:29Z

←Older revision		Revision as of 11:39, 25 December 2019
Line 1:		Line 1:

	==Galectin-8 N-terminal domain carbohydrate recognition domain==		==Galectin-8 N-terminal domain carbohydrate recognition domain==
-	<StructureSection load='5gzg' size='340' side='right' caption='[[5gzg]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5gzg' size='340' side='right'caption='[[5gzg]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gzg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GZG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GZG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gzg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GZG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GZG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LAT:BETA-LACTOSE'>LAT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LAT:BETA-LACTOSE'>LAT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gzc\|5gzc]], [[5gzd\|5gzd]], [[5gze\|5gze]], [[5gzf\|5gzf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gzc\|5gzc]], [[5gzd\|5gzd]], [[5gze\|5gze]], [[5gzf\|5gzf]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LGALS8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5gzg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gzg OCA], [http://pdbe.org/5gzg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gzg RCSB], [http://www.ebi.ac.uk/pdbsum/5gzg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gzg ProSAT]</span></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=5gzg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gzg OCA], [http://pdbe.org/5gzg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gzg RCSB], [http://www.ebi.ac.uk/pdbsum/5gzg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gzg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/LEG8_HUMAN LEG8_HUMAN]] Lectin with a marked preference for 3'-O-sialylated and 3'-O-sulfated glycans.<ref>PMID:21288902</ref>		[[http://www.uniprot.org/uniprot/LEG8_HUMAN LEG8_HUMAN]] Lectin with a marked preference for 3'-O-sialylated and 3'-O-sulfated glycans.<ref>PMID:21288902</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Galectin-8 (Gal-8) plays a significant role in normal immunological function as well as in cancer. This lectin contains two carbohydrate recognition domains (CRD) connected by a peptide linker. The N-terminal CRD determines ligand binding specificity, whereas the linker has been proposed to regulate overall Gal-8 function, including multimerization and biological activity. Here, we crystallized the Gal-8 N-terminal CRD with the peptide linker using a crystallization condition that contains Ni(2+). The Ni(2+) ion was found to be complexed between two CRDs via crystal packing contacts. The coordination between Ni(2+) and Asp25 plays an indirect role in determining the structure of beta-strand F0 and in influencing the linker conformation which could not be defined due to its dynamic nature. The linker was also shortened in situ and crystallized under a different condition, leading to a higher resolution structure refined to 1.08 A. This crystal structure allowed definition of a short portion of the linker interacting with the Gal-8 N-terminal tail via ionic interactions and hydrogen bonds. Observation of two Gal-8 N-terminal CRD structures implies that the N-terminal tail and the linker may influence each other's conformation. In addition, under specific crystallization conditions, glycerol could replace lactose and was observed at the carbohydrate binding site. However, glycerol did not show inhibition activity in hemagglutination assay.
		+
		+	Crystallization of Galectin-8 Linker Reveals Intricate Relationship between the N-terminal Tail and the Linker.,Si Y, Wang Y, Gao J, Song C, Feng S, Zhou Y, Tai G, Su J Int J Mol Sci. 2016 Dec 12;17(12). pii: ijms17122088. doi: 10.3390/ijms17122088. PMID:27973456<ref>PMID:27973456</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5gzg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galectin 3D structures\|Galectin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Si, Y L]]		[[Category: Si, Y L]]
	[[Category: Su, J Y]]		[[Category: Su, J Y]]
	[[Category: Galectin-8 n-terminal domain carbohydrate recognition domain]]		[[Category: Galectin-8 n-terminal domain carbohydrate recognition domain]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

OCA at 21:39, 22 December 2016

2016-12-22T21:39:28Z

←Older revision		Revision as of 21:39, 22 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gzg is ~~ON HOLD until Paper Publication~~	+	==Galectin-8 N-terminal domain carbohydrate recognition domain==
-		+	<StructureSection load='5gzg' size='340' side='right' caption='[[5gzg]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: Su, J.Y., Si, Y.L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5gzg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GZG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GZG FirstGlance]. <br>
-	~~Description~~: ~~Galectin~~-~~8 N-terminal domain carbohydrate recognition domain~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LAT:BETA-LACTOSE'>LAT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gzc\|5gzc]], [[5gzd\|5gzd]], [[5gze\|5gze]], [[5gzf\|5gzf]]</td></tr>
-	[[Category: Si, Y.L]]	+	<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=5gzg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gzg OCA], [http://pdbe.org/5gzg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gzg RCSB], [http://www.ebi.ac.uk/pdbsum/5gzg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gzg ProSAT]</span></td></tr>
-	[[Category: Su, J.Y]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LEG8_HUMAN LEG8_HUMAN]] Lectin with a marked preference for 3'-O-sialylated and 3'-O-sulfated glycans.<ref>PMID:21288902</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Si, Y L]]
		+	[[Category: Su, J Y]]
		+	[[Category: Galectin-8 n-terminal domain carbohydrate recognition domain]]
		+	[[Category: Sugar binding protein]]

OCA at 13:34, 9 December 2016

2016-12-09T13:34:59Z

←Older revision		Revision as of 13:34, 9 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Su, J.Y., Si, Y.L.		Authors: Su, J.Y., Si, Y.L.

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

2016-10-05T16:21:35Z

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

←Older revision

Revision as of 16:21, 5 October 2016

OCA: New page: '''Unreleased structure''' The entry 5gzg is ON HOLD Authors: Su, J.Y., Si, Y.L. Description: Galectin-8 N-terminal domain carbohydrate recognition domain [[Category: Unreleased Struct...

2016-10-05T16:21:34Z

New page: '''Unreleased structure''' The entry 5gzg is ON HOLD Authors: Su, J.Y., Si, Y.L. Description: Galectin-8 N-terminal domain carbohydrate recognition domain [[Category: Unreleased Struct...

New page

'''Unreleased structure'''

The entry 5gzg is ON HOLD

Authors: Su, J.Y., Si, Y.L.

Description: Galectin-8 N-terminal domain carbohydrate recognition domain
[[Category: Unreleased Structures]]
[[Category: Si, Y.L]]
[[Category: Su, J.Y]]