6y5x - Revision history

OCA at 13:19, 24 January 2024

OCA — Wed, 24 Jan 2024 13:19:59 GMT

←Older revision		Revision as of 13:19, 24 January 2024
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	<StructureSection load='6y5x' size='340' side='right'caption='[[6y5x]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6y5x' size='340' side='right'caption='[[6y5x]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6y5x]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Nj-pymv~~-2013 ~~Nj-pymv~~-2013]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y5X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6Y5X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y5x]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/New_Jersey_polyomavirus-2013 New Jersey polyomavirus-2013]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y5X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y5X FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.3Å</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=1497391 NJ-PyMv-2013])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=6y5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y5x OCA], [~~http~~://pdbe.org/6y5x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6y5x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6y5x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6y5x 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=6y5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y5x OCA], [https://pdbe.org/6y5x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y5x RCSB], [https://www.ebi.ac.uk/pdbsum/6y5x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y5x ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A024B5J2_9POLY A0A024B5J2_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 6y5x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6y5x" 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: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Nj-pymv~~-2013]]	+	[[Category: New Jersey polyomavirus-2013]]
-	[[Category: Rustmeier~~, N H~~]]	+	[[Category: Rustmeier NH]]
-	[[Category: Stehle, T]]	+	[[Category: Stehle T]]
-	[[Category: Stroh~~, L J]]~~	+	[[Category: Stroh LJ]]
-	~~[[Category: Major capsid protein]]~~	+
-	~~[[Category: Polyomavirus]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 10:07, 12 August 2020

OCA — Wed, 12 Aug 2020 10:07:54 GMT

←Older revision		Revision as of 10:07, 12 August 2020
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	==Structure of apo New Jersey Polyomavirus VP1==		==Structure of apo New Jersey Polyomavirus VP1==
-	<StructureSection load='6y5x' size='340' side='right'caption='[[6y5x]]' scene=''>	+	<StructureSection load='6y5x' size='340' side='right'caption='[[6y5x]], [[Resolution\|resolution]] 2.30Å' 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=6Y5X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y5X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y5x]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Nj-pymv-2013 Nj-pymv-2013]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y5X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y5X 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=6y5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y5x OCA], [http://pdbe.org/6y5x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y5x RCSB], [http://www.ebi.ac.uk/pdbsum/6y5x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y5x ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1497391 NJ-PyMv-2013])</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=6y5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y5x OCA], [http://pdbe.org/6y5x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y5x RCSB], [http://www.ebi.ac.uk/pdbsum/6y5x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y5x ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Asymptomatic infections with polyomaviruses in humans are common, but these small viruses can cause severe diseases in immunocompromised hosts. New Jersey polyomavirus (NJPyV) was identified via a muscle biopsy in an organ transplant recipient with systemic vasculitis, myositis, and retinal blindness, and human polyomavirus 12 (HPyV12) was detected in human liver tissue. The evolutionary origins and potential diseases are not well understood for either virus. In order to define their receptor engagement strategies, we first used nuclear magnetic resonance (NMR) spectroscopy to establish that the major capsid proteins (VP1) of both viruses bind to sialic acid in solution. We then solved crystal structures of NJPyV and HPyV12 VP1 alone and in complex with sialylated glycans. NJPyV employs a novel binding site for a alpha2,3-linked sialic acid, whereas HPyV12 engages terminal alpha2,3- or alpha2,6-linked sialic acids in an exposed site similar to that found in Trichodysplasia spinulosa-associated polyomavirus (TSPyV). Gangliosides or glycoproteins, featuring in mammals usually terminal sialic acids, are therefore receptor candidates for both viruses. Structural analyses show that the sialic acid-binding site of NJPyV is conserved in chimpanzee polyomavirus (ChPyV) and that the sialic acid-binding site of HPyV12 is widely used across the entire polyomavirus family, including mammalian and avian polyomaviruses. A comparison with other polyomavirus-receptor complex structures shows that their capsids have evolved to generate several physically distinct virus-specific receptor-binding sites that can all specifically engage sialylated glycans through a limited number of contacts. Small changes in each site may have enabled host-switching events during the evolution of polyomaviruses.IMPORTANCE Virus attachment to cell surface receptors is critical for productive infection. In this study, we have used a structure-based approach to investigate the cell surface recognition event for New Jersey polyomavirus (NJPyV) and human polyomavirus 12 (HPyV12). These viruses belong to the polyomavirus family, whose members target different tissues and hosts, including mammals, birds, fish, and invertebrates. Polyomaviruses are nonenveloped viruses, and the receptor-binding site is located in their capsid protein VP1. The NJPyV capsid features a novel sialic acid-binding site that is shifted in comparison to other structurally characterized polyomaviruses but shared with a closely related simian virus. In contrast, HPyV12 VP1 engages terminal sialic acids in a manner similar to the human Trichodysplasia spinulosa-associated polyomavirus. Our structure-based phylogenetic analysis highlights that even distantly related avian polyomaviruses possess the same exposed sialic acid-binding site. These findings complement phylogenetic models of host-virus codivergence and may also reflect past host-switching events.
		+
		+	Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family.,Stroh LJ, Rustmeier NH, Blaum BS, Botsch J, Rossler P, Wedekink F, Lipkin WI, Mishra N, Stehle T mBio. 2020 Jul 28;11(4). pii: mBio.00745-20. doi: 10.1128/mBio.00745-20. PMID:32723915<ref>PMID:32723915</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y5x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rustmeier NH]]	+	[[Category: Nj-pymv-2013]]
-	[[Category: Stehle T]]	+	[[Category: Rustmeier, N H]]
-	[[Category: Stroh LJ]]	+	[[Category: Stehle, T]]
		+	[[Category: Stroh, L J]]
		+	[[Category: Major capsid protein]]
		+	[[Category: Polyomavirus]]
		+	[[Category: Viral protein]]

OCA at 14:11, 8 July 2020

OCA — Wed, 08 Jul 2020 14:11:24 GMT

←Older revision		Revision as of 14:11, 8 July 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6y5x is ~~ON HOLD until Paper Publication~~	+	==Structure of apo New Jersey Polyomavirus VP1==
-		+	<StructureSection load='6y5x' size='340' side='right'caption='[[6y5x]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y5X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y5X 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=6y5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y5x OCA], [http://pdbe.org/6y5x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y5x RCSB], [http://www.ebi.ac.uk/pdbsum/6y5x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y5x ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Rustmeier NH]]
		+	[[Category: Stehle T]]
		+	[[Category: Stroh LJ]]

OCA at 06:14, 11 March 2020

OCA — Wed, 11 Mar 2020 06:14:05 GMT

←Older revision		Revision as of 06:14, 11 March 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y5x is ON HOLD	+	The entry 6y5x is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6y5x" [edit=sysop:move=sysop]

OCA — Wed, 04 Mar 2020 05:46:02 GMT

Protected "6y5x" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:46, 4 March 2020

OCA: New page: '''Unreleased structure''' The entry 6y5x is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Mar 2020 05:46:01 GMT

New page: '''Unreleased structure''' The entry 6y5x is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6y5x is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]