4x0y - Revision history

OCA at 10:45, 10 January 2024

2024-01-10T10:45:49Z

←Older revision		Revision as of 10:45, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x0y]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/JC_polyomavirus_type_3 JC polyomavirus type 3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X0Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x0y]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/JC_polyomavirus_type_3 JC polyomavirus type 3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X0Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=4x0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0y OCA], [https://pdbe.org/4x0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x0y RCSB], [https://www.ebi.ac.uk/pdbsum/4x0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0y 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=4x0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0y OCA], [https://pdbe.org/4x0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x0y RCSB], [https://www.ebi.ac.uk/pdbsum/4x0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0y ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:06, 12 April 2023

2023-04-12T21:06:15Z

←Older revision		Revision as of 21:06, 12 April 2023
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	==JC polyomavirus VP1 from a genotype 3 strain==		==JC polyomavirus VP1 from a genotype 3 strain==
-	<StructureSection load='4x0y' size='340' side='right' caption='[[4x0y]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='4x0y' size='340' side='right'caption='[[4x0y]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x0y]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Jc_polyomavirus_type_3 Jc~~ polyomavirus type 3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4X0Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x0y]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/JC_polyomavirus_type_3 JC polyomavirus type 3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X0Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nxd\|3nxd]], [[3nxg\|3nxg]]</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=4x0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0y OCA], [https://pdbe.org/4x0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x0y RCSB], [https://www.ebi.ac.uk/pdbsum/4x0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0y ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=804310 JC polyomavirus type 3])</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=4x0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0y OCA], [~~http~~://pdbe.org/4x0y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4x0y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4x0y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0y ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/P90498_POVJC P90498_POVJC]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4x0y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4x0y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Jc polyomavirus type 3]]	+	[[Category: JC polyomavirus type 3]]
-	[[Category: ~~Stehle, T~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Stroh, L J~~]]	+	[[Category: Stehle T]]
-	[[Category: ~~Beta-sandwich]]~~	+	[[Category: Stroh LJ]]
-	~~[[Category: Jelly-roll]]~~	+
-	~~[[Category: Viral capsid protein]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 06:50, 31 January 2018

2018-01-31T06:50:49Z

←Older revision		Revision as of 06:50, 31 January 2018
Line 3:		Line 3:
	<StructureSection load='4x0y' size='340' side='right' caption='[[4x0y]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4x0y' size='340' side='right' caption='[[4x0y]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x0y]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x0y]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Jc_polyomavirus_type_3 Jc polyomavirus type 3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nxd\|3nxd]], [[3nxg\|3nxg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nxd\|3nxd]], [[3nxg\|3nxg]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=804310 JC polyomavirus type 3])</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=4x0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0y OCA], [http://pdbe.org/4x0y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x0y RCSB], [http://www.ebi.ac.uk/pdbsum/4x0y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0y 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=4x0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0y OCA], [http://pdbe.org/4x0y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x0y RCSB], [http://www.ebi.ac.uk/pdbsum/4x0y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0y ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Jc polyomavirus type 3]]
	[[Category: Stehle, T]]		[[Category: Stehle, T]]
	[[Category: Stroh, L J]]		[[Category: Stroh, L J]]

OCA at 01:56, 10 March 2017

2017-03-10T01:56:42Z

←Older revision		Revision as of 01:56, 10 March 2017
Line 1:		Line 1:
		+
	==JC polyomavirus VP1 from a genotype 3 strain==		==JC polyomavirus VP1 from a genotype 3 strain==
	<StructureSection load='4x0y' size='340' side='right' caption='[[4x0y]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4x0y' size='340' side='right' caption='[[4x0y]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nxd\|3nxd]], [[3nxg\|3nxg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nxd\|3nxd]], [[3nxg\|3nxg]]</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=4x0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x0y RCSB], [http://www.ebi.ac.uk/pdbsum/4x0y 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=4x0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0y OCA], [http://pdbe.org/4x0y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x0y RCSB], [http://www.ebi.ac.uk/pdbsum/4x0y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0y ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4x0y" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:46, 22 April 2015

2015-04-22T12:46:11Z

←Older revision		Revision as of 12:46, 22 April 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==JC polyomavirus VP1 from a genotype 3 strain==
		+	<StructureSection load='4x0y' size='340' side='right' caption='[[4x0y]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4x0y]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0Y FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nxd\|3nxd]], [[3nxg\|3nxg]]</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=4x0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x0y RCSB], [http://www.ebi.ac.uk/pdbsum/4x0y PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The human JC polyomavirus (JCPyV) establishes an asymptomatic, persistent infection in the kidney of the majority of the population, and is the causative agent of the fatal, demyelinating disease progressive multifocal leukoencephalopathy (PML) in immunosuppressed individuals. The Mad-1 strain of JCPyV, a brain isolate, was shown earlier to require alpha2,6-linked sialic acid on the LSTc glycan for attachment to host cells. In contrast, a JCPyV kidney isolate Type 3 strain, "WT3", has been reported to interact with sialic acid-containing gangliosides, but the role of these glycans in JCPyV infection has remained unclear. To help rationalize these findings and probe the effects of strain-specific differences on receptor binding, we performed a comprehensive analysis of the glycan receptor specificities of these two representative JCPyV strains using high-resolution X-ray crystallography and NMR spectroscopy, and correlated these data with infectivity assays. We show here that capsid proteins of Mad-1 and WT3 JCPyV can both engage LSTc as well as multiple sialylated gangliosides. However, the binding affinities exhibit subtle differences, with the highest affinity observed for LSTc. Engagement of LSTc is a prerequisite for functional receptor engagement while the weaker-binding gangliosides are not required for productive infection. Our findings highlight the complexity of virus-carbohydrate interactions and demonstrate that subtle differences in binding affinities, rather than the binding event alone, help determine tissue tropism and viral pathogenesis. IMPORTANCE: Viral infection is initiated by attachment to receptors on host cells, and this event plays an important role in viral disease. We investigated the receptor-binding properties of human JC polyomavirus (JCPyV), a virus that resides in the kidney of the majority of the population and can cause the fatal, demyelinating disease progressive multifocal leukoencephalopathy (PML) in the brain of immunosuppressed individuals. JCPyV has been reported to interact with multiple carbohydrate receptors, and we sought to clarify how the interactions between JCPyV and cellular carbohydrate receptors influenced infection. Here we demonstrate that JCPyV can engage numerous sialylated carbohydrate receptors. However, the virus displays preferential binding to LSTc, and only LSTc mediates a productive infection. Our findings demonstrate that subtle differences in binding affinity, rather than receptor engagement alone, are a key determinant of viral infection.

-	~~The entry 4x0y is ON HOLD until Paper Publication~~	+	Increased Affinity of JC Polyomavirus Capsid for LSTc Over Other Sialylated Glycans Is a Major Determinant of Infectivity.,Stroh LJ, Maginnis MS, Blaum BS, Nelson CD, Neu U, Gee GV, O'Hara BA, Motamedi N, DiMaio D, Atwood WJ, Stehle T J Virol. 2015 Apr 8. pii: JVI.00489-15. PMID:25855729<ref>PMID:25855729</ref>

-	~~Authors: Stroh~~, L.J.~~, Stehle, T~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description:~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
-	~~[[Category: Stroh, L.J]]~~	+	__TOC__
		+	</StructureSection>
	[[Category: Stehle, T]]		[[Category: Stehle, T]]
		+	[[Category: Stroh, L J]]
		+	[[Category: Beta-sandwich]]
		+	[[Category: Jelly-roll]]
		+	[[Category: Viral capsid protein]]
		+	[[Category: Viral protein]]

OCA at 20:18, 24 December 2014

2014-12-24T20:18:48Z

←Older revision		Revision as of 20:18, 24 December 2014
Line 5:		Line 5:
	Authors: Stroh, L.J., Stehle, T.		Authors: Stroh, L.J., Stehle, T.

-	Description:	+	Description:
		+	[[Category: Unreleased Structures]]
		+	[[Category: Stroh, L.J]]
		+	[[Category: Stehle, T]]

OCA: Protected "4x0y" [edit=sysop:move=sysop]

2014-12-03T08:44:39Z

Protected "4x0y" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:44, 3 December 2014

OCA: New page: '''Unreleased structure''' The entry 4x0y is ON HOLD until Paper Publication Authors: Stroh, L.J., Stehle, T. Description:

2014-12-03T08:44:38Z

New page: '''Unreleased structure''' The entry 4x0y is ON HOLD until Paper Publication Authors: Stroh, L.J., Stehle, T. Description:

New page

'''Unreleased structure'''

The entry 4x0y is ON HOLD until Paper Publication

Authors: Stroh, L.J., Stehle, T.

Description: