4por - Revision history

OCA at 17:19, 20 September 2023

OCA — Wed, 20 Sep 2023 17:19:53 GMT

←Older revision		Revision as of 17:19, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4por]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_polyomavirus_9 Human polyomavirus 9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4POR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4POR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4por]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_polyomavirus_9 Human polyomavirus 9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4POR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4POR FirstGlance]. <br>
-	</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</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]] 2.09Å</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</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=4por FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4por OCA], [https://pdbe.org/4por PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4por RCSB], [https://www.ebi.ac.uk/pdbsum/4por PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4por ProSAT]</span></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=4por FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4por OCA], [https://pdbe.org/4por PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4por RCSB], [https://www.ebi.ac.uk/pdbsum/4por PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4por ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:22, 8 February 2023

OCA — Wed, 08 Feb 2023 07:22:03 GMT

←Older revision		Revision as of 07:22, 8 February 2023
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	==Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose==		==Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose==
-	<StructureSection load='4por' size='340' side='right' caption='[[4por]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='4por' size='340' side='right'caption='[[4por]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4por]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human_polyomavirus_9 Human polyomavirus 9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4POR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4POR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4por]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_polyomavirus_9 Human polyomavirus 9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4POR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4POR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO~~</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA~~</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene><~~/td></tr>~~	+	</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>
-	~~<tr id~~='~~NonStdRes'><td class~~=~~"sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res~~:~~]]</b~~></~~td><td class="sblockDat"~~><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=4por FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4por OCA], [https://pdbe.org/4por PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4por RCSB], [https://www.ebi.ac.uk/pdbsum/4por PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4por ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mby\|4mby]], [[4fmi\|4fmi]], [[4poq\|4poq]], [[4pos\|4pos]], [[4pot\|4pot]]</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gp3, vp1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=943908 Human polyomavirus 9])</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=4por FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4por OCA], [~~http~~://pdbe.org/4por PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4por RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4por PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4por ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E9NQ90_9POLY E9NQ90_9POLY]
	<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 4por" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4por" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human polyomavirus 9]]		[[Category: Human polyomavirus 9]]
-	[[Category: ~~Khan, Z M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Stehle, T~~]]	+	[[Category: Khan ZM]]
-	[[Category: ~~Capsid formation]]~~	+	[[Category: Stehle T]]
-	~~[[Category: Carbohydrate]]~~	+
-	~~[[Category: Jelly roll fold]]~~	+
-	~~[[Category: Receptor interaction]]~~	+
-	~~[[Category: Sialyloligosaccharide]]~~	+
-	~~[[Category: Viral coat protein]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 10:36, 11 August 2016

OCA — Thu, 11 Aug 2016 10:36:20 GMT

←Older revision		Revision as of 10:36, 11 August 2016
Line 1:		Line 1:
		+
	==Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose==		==Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose==
	<StructureSection load='4por' size='340' side='right' caption='[[4por]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='4por' size='340' side='right' caption='[[4por]], [[Resolution\|resolution]] 2.09Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mby\|4mby]], [[4fmi\|4fmi]], [[4poq\|4poq]], [[4pos\|4pos]], [[4pot\|4pot]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mby\|4mby]], [[4fmi\|4fmi]], [[4poq\|4poq]], [[4pos\|4pos]], [[4pot\|4pot]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gp3, vp1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=943908 Human polyomavirus 9])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gp3, vp1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=943908 Human polyomavirus 9])</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=4por FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4por OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4por RCSB], [http://www.ebi.ac.uk/pdbsum/4por PDBsum]</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=4por FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4por OCA], [http://pdbe.org/4por PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4por RCSB], [http://www.ebi.ac.uk/pdbsum/4por PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4por ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4por" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:07, 26 November 2014

OCA — Wed, 26 Nov 2014 06:07:05 GMT

←Older revision		Revision as of 06:07, 26 November 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4por\| PDB=4por \| SCENE= }}~~	+	==Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose==
-	===Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose===	+	<StructureSection load='4por' size='340' side='right' caption='[[4por]], [[Resolution\|resolution]] 2.09Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4por]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_polyomavirus_9 Human polyomavirus 9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4POR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4POR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mby\|4mby]], [[4fmi\|4fmi]], [[4poq\|4poq]], [[4pos\|4pos]], [[4pot\|4pot]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gp3, vp1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=943908 Human polyomavirus 9])</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=4por FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4por OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4por RCSB], [http://www.ebi.ac.uk/pdbsum/4por PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human polyomavirus 9 (HPyV9) is a closely related homologue of simian B-lymphotropic polyomavirus (LPyV). In order to define the architecture and receptor binding properties of HPyV9, we solved high-resolution crystal structures of its major capsid protein, VP1, in complex with three putative oligosaccharide receptors identified by glycan microarray screening. Comparison of the properties of HPyV9 VP1 with the known structure and glycan-binding properties of LPyV VP1 revealed that both viruses engage short sialylated oligosaccharides, but small yet important differences in specificity were detected. Surprisingly, HPyV9 VP1 preferentially binds sialyllactosamine compounds terminating in 5-N-glycolyl neuraminic acid (Neu5Gc) over those terminating in 5-N-acetyl neuraminic acid (Neu5Ac), whereas LPyV does not exhibit such a preference. The structural analysis demonstrated that HPyV9 makes specific contacts, via hydrogen bonds, with the extra hydroxyl group present in Neu5Gc. An equivalent hydrogen bond cannot be formed by LPyV VP1. IMPORTANCE: The most common sialic acid in humans is 5-N-acetyl neuraminic acid (Neu5Ac), but various modifications give rise to more than 50 different sialic acid variants that decorate the cell surface. Unlike most mammals, humans cannot synthesize the sialic acid variant 5-N-glycolyl neuraminic acid (Neu5Gc) due to a gene defect. Humans can, however, still acquire this compound from dietary sources. The role of Neu5Gc in receptor engagement and in defining viral tropism is only beginning to emerge, and structural analyses defining the differences in specificity for Neu5Ac and Neu5Gc are still rare. Using glycan microarray screening and high-resolution protein crystallography, we have examined the receptor specificity of a recently discovered human polyomavirus, HPyV9, and compared it to that of the closely related simian polyomavirus LPyV. Our study highlights critical differences in the specificities of both viruses, contributing to an enhanced understanding of the principles that underlie pathogen selectivity for modified sialic acids.

-	~~==About this Structure==~~	+	Crystallographic and glycan microarray analysis of human polyomavirus 9 VP1 identifies N-glycolyl neuraminic acid as a receptor candidate.,Khan ZM, Liu Y, Neu U, Gilbert M, Ehlers B, Feizi T, Stehle T J Virol. 2014 Jun;88(11):6100-11. doi: 10.1128/JVI.03455-13. Epub 2014 Mar 19. PMID:24648448<ref>PMID:24648448</ref>
-	~~[[4por]] is~~ a 10 ~~chain structure~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id~~=~~4POR OCA~~].	+
-	[[Category: Khan, Z M.]]	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: Stehle, T.]]	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human polyomavirus 9]]
		+	[[Category: Khan, Z M]]
		+	[[Category: Stehle, T]]
	[[Category: Capsid formation]]		[[Category: Capsid formation]]
	[[Category: Carbohydrate]]		[[Category: Carbohydrate]]

OCA at 06:48, 9 April 2014

OCA — Wed, 09 Apr 2014 06:48:33 GMT

←Older revision		Revision as of 06:48, 9 April 2014
Line 1:		Line 1:
-	'~~''Unreleased structure'''~~	+	{{STRUCTURE_4por\| PDB=4por \| SCENE= }}
		+	===Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose===

-	~~The entry~~ 4por is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4por]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4POR OCA].
-	~~Authors~~: Khan, Z.M., Stehle, T.	+	[[Category: Khan, Z M.]]
-		+	[[Category: Stehle, T.]]
-	~~Description~~: ~~Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose~~	+	[[Category: Capsid formation]]
		+	[[Category: Carbohydrate]]
		+	[[Category: Jelly roll fold]]
		+	[[Category: Receptor interaction]]
		+	[[Category: Sialyloligosaccharide]]
		+	[[Category: Viral coat protein]]
		+	[[Category: Viral protein]]

OCA: Protected "4por" [edit=sysop:move=sysop]

OCA — Wed, 12 Mar 2014 12:32:40 GMT

Protected "4por" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:32, 12 March 2014

OCA: New page: '''Unreleased structure''' The entry 4por is ON HOLD Authors: Khan, Z.M., Stehle, T. Description: Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose

OCA — Wed, 12 Mar 2014 12:32:39 GMT

New page: '''Unreleased structure''' The entry 4por is ON HOLD Authors: Khan, Z.M., Stehle, T. Description: Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose

New page

'''Unreleased structure'''

The entry 4por is ON HOLD

Authors: Khan, Z.M., Stehle, T.

Description: Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose