1sie - Revision history

OCA at 08:32, 1 May 2024

OCA — Wed, 01 May 2024 08:32:14 GMT

←Older revision		Revision as of 08:32, 1 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mouse_polyomavirus_(strain_p16_small-plaque) Mouse polyomavirus (strain p16 small-plaque)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SIE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mouse_polyomavirus_(strain_p16_small-plaque) Mouse polyomavirus (strain p16 small-plaque)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SIE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GAL:BETA~~-~~D-GALACTOSE'>GAL</scene>~~, ~~<scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 3.65Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [https://pdbe.org/1sie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [https://www.ebi.ac.uk/pdbsum/1sie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sie 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=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [https://pdbe.org/1sie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [https://www.ebi.ac.uk/pdbsum/1sie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sie ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/VP1_POVMP VP1_POVMP]] Forms an icosahedral capsid with a T=7 symmetry and a 40 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with terminal alpha(2,3)-linked sialic acids on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through caveolin-mediated endocytosis. Once attached, the virion is internalized by caveolin-mediated endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).	+	[https://www.uniprot.org/uniprot/VP1_POVMP VP1_POVMP] Forms an icosahedral capsid with a T=7 symmetry and a 40 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with terminal alpha(2,3)-linked sialic acids on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through caveolin-mediated endocytosis. Once attached, the virion is internalized by caveolin-mediated endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1sie ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1sie ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: Murine polyomavirus recognizes (alpha2,3)-linked alpha-5-N-acetylneuraminic acid (sialic acid) on the surface of susceptible cells. While all strains bind to straight-chain receptors terminating in (alpha2,3)-linked sialic acid, some strains also bind to branched oligosaccharides that carry a second, (alpha2,6)-linked sialic acid. The ability to bind to these branched-chain receptors correlates with a single amino acid mutation at position 91 on the outer surface of the major capsid protein, VP1, and with a significant decrease in tumorigenicity. RESULTS: We have determined the structures of polyomavirus strain P16, which bears a glycine at position 91, in complex with model compounds for both straight-chain and branched-chain sialoglycoconjugates. The structures have been refined to a resolution of 3.65 degree. The ligands bind to a shallow groove on the surface of VP1. The sialic acid-(alpha2,3)-galactose moiety, which is common to both compounds, has specific and identical contacts. The additional (alpha2,6)-linked sialic acid moiety of the branched-chain receptor fragment fits into a surface pocket, but it has high thermal factors and does not form hydrogen bonds to groups on VP1. Data collected from crystals soaked at different oligosaccharide concentrations establish that both receptor fragments have similar, low affinities (dissociation constants in the range 5-10 mM) for the P16 virus, consistent with the interactions seen in the two complexes. CONCLUSION: The oligosaccharide-binding groove is complementary to the shape of the bound glycan, but there are relatively few hydrogen bonds between glycan and protein. Thus, the nature of the glycosidic linkages appears to be the principal determinant of specificity, rather than the position of particular hydroxyl groups. The low receptor affinity may be important for avoiding inhibition of viral release by retention on surface receptors of infected cells. Evidence suggests that strains with still greater pathogenicity are likely to have even weaker affinity.
-
-	Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments.,Stehle T, Harrison SC Structure. 1996 Feb 15;4(2):183-94. PMID:8805524<ref>PMID:8805524</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1sie" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]		*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Harrison~~, S C~~]]	+	[[Category: Harrison SC]]
-	[[Category: Stehle, T]]	+	[[Category: Stehle T]]
-	~~[[Category: Coat protein]]~~	+
-	~~[[Category: Icosahedral virus]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 10:18, 12 January 2022

OCA — Wed, 12 Jan 2022 10:18:25 GMT

←Older revision		Revision as of 10:18, 12 January 2022
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	<SX load='1sie' size='340' side='right' viewer='molstar' caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>		<SX load='1sie' size='340' side='right' viewer='molstar' caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mouse_polyomavirus_(strain_p16_small-plaque) Mouse polyomavirus (strain p16 small-plaque)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1SIE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mouse_polyomavirus_(strain_p16_small-plaque) Mouse polyomavirus (strain p16 small-plaque)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SIE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [~~http~~://pdbe.org/1sie PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1sie PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1sie ProSAT]</span></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=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [https://pdbe.org/1sie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [https://www.ebi.ac.uk/pdbsum/1sie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sie ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VP1_POVMP VP1_POVMP]] Forms an icosahedral capsid with a T=7 symmetry and a 40 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with terminal alpha(2,3)-linked sialic acids on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through caveolin-mediated endocytosis. Once attached, the virion is internalized by caveolin-mediated endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).	+	[[https://www.uniprot.org/uniprot/VP1_POVMP VP1_POVMP]] Forms an icosahedral capsid with a T=7 symmetry and a 40 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with terminal alpha(2,3)-linked sialic acids on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through caveolin-mediated endocytosis. Once attached, the virion is internalized by caveolin-mediated endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:39, 10 April 2020

OCA — Fri, 10 Apr 2020 16:39:53 GMT

←Older revision		Revision as of 16:39, 10 April 2020
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	<SX load='1sie' size='340' side='right' viewer='molstar' caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>		<SX load='1sie' size='340' side='right' viewer='molstar' caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mouse_polyomavirus_(strain_p16_small-plaque) Mouse polyomavirus (strain p16 small-plaque)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SIE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mouse_polyomavirus_(strain_p16_small-plaque) Mouse polyomavirus (strain p16 small-plaque)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SIE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [http://pdbe.org/1sie PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [http://www.ebi.ac.uk/pdbsum/1sie PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sie ProSAT]</span></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=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [http://pdbe.org/1sie PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [http://www.ebi.ac.uk/pdbsum/1sie PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sie ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Virus coat ~~protein~~\|Virus coat ~~protein~~]]	+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:21, 5 March 2020

OCA — Thu, 05 Mar 2020 04:21:53 GMT

←Older revision		Revision as of 04:21, 5 March 2020
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	==MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE==		==MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE==
-	<~~StructureSection~~ load='1sie' size='340' side='right'caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>	+	<SX load='1sie' size='340' side='right' viewer='molstar' caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mouse_polyomavirus_(strain_p16_small-plaque) Mouse polyomavirus (strain p16 small-plaque)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SIE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mouse_polyomavirus_(strain_p16_small-plaque) Mouse polyomavirus (strain p16 small-plaque)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SIE FirstGlance]. <br>
Line 34:		Line 34:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Harrison, S C]]		[[Category: Harrison, S C]]

OCA at 14:13, 18 December 2019

OCA — Wed, 18 Dec 2019 14:13:16 GMT

←Older revision		Revision as of 14:13, 18 December 2019
Line 1:		Line 1:

	==MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE==		==MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE==
-	<StructureSection load='1sie' size='340' side='right' caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>	+	<StructureSection load='1sie' size='340' side='right'caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mouse_polyomavirus_(strain_p16_small-plaque) Mouse polyomavirus (strain p16 small-plaque)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SIE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mouse_polyomavirus_(strain_p16_small-plaque) Mouse polyomavirus (strain p16 small-plaque)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SIE FirstGlance]. <br>
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Harrison, S C]]		[[Category: Harrison, S C]]
	[[Category: Stehle, T]]		[[Category: Stehle, T]]

OCA at 07:53, 14 March 2018

OCA — Wed, 14 Mar 2018 07:53:28 GMT

←Older revision		Revision as of 07:53, 14 March 2018
Line 1:		Line 1:
		+
	==MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE==		==MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE==
	<StructureSection load='1sie' size='340' side='right' caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>		<StructureSection load='1sie' size='340' side='right' caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mpyv Mpyv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SIE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mouse_polyomavirus_(strain_p16_small-plaque) Mouse polyomavirus (strain p16 small-plaque)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SIE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [http://pdbe.org/1sie PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [http://www.ebi.ac.uk/pdbsum/1sie PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sie 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=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [http://pdbe.org/1sie PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [http://www.ebi.ac.uk/pdbsum/1sie PDBsum]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/si/1sie_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/si/1sie_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mpyv]]
	[[Category: Harrison, S C]]		[[Category: Harrison, S C]]
	[[Category: Stehle, T]]		[[Category: Stehle, T]]

OCA at 05:17, 7 February 2016

OCA — Sun, 07 Feb 2016 05:17:20 GMT

←Older revision		Revision as of 05:17, 7 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1sie ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:12, 9 September 2015

OCA — Wed, 09 Sep 2015 22:12:39 GMT

←Older revision		Revision as of 22:12, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1sie' size='340' side='right' caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>		<StructureSection load='1sie' size='340' side='right' caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Viruses Viruses~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SIE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mpyv Mpyv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SIE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [http://www.ebi.ac.uk/pdbsum/1sie 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=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [http://pdbe.org/1sie PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [http://www.ebi.ac.uk/pdbsum/1sie PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~COA1_POVMP COA1_POVMP~~]] Forms an icosahedral capsid with a T=7 symmetry and a 40 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with terminal alpha(2,3)-linked sialic acids on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through caveolin-mediated endocytosis. Once attached, the virion is internalized by caveolin-mediated endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).	+	[[http://www.uniprot.org/uniprot/VP1_POVMP VP1_POVMP]] Forms an icosahedral capsid with a T=7 symmetry and a 40 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with terminal alpha(2,3)-linked sialic acids on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through caveolin-mediated endocytosis. Once attached, the virion is internalized by caveolin-mediated endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 27:
	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 1sie" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Viruses~~]]	+	[[Category: Mpyv]]
	[[Category: Harrison, S C]]		[[Category: Harrison, S C]]
	[[Category: Stehle, T]]		[[Category: Stehle, T]]

OCA at 08:07, 24 December 2014

OCA — Wed, 24 Dec 2014 08:07:42 GMT

←Older revision		Revision as of 08:07, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SIE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SIE FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [http://www.ebi.ac.uk/pdbsum/1sie 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=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [http://www.ebi.ac.uk/pdbsum/1sie PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/COA1_POVMP COA1_POVMP]] Forms an icosahedral capsid with a T=7 symmetry and a 40 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with terminal alpha(2,3)-linked sialic acids on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through caveolin-mediated endocytosis. Once attached, the virion is internalized by caveolin-mediated endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Viruses]]		[[Category: Viruses]]
-	[[Category: Harrison, S C.]]	+	[[Category: Harrison, S C]]
-	[[Category: Stehle, T.]]	+	[[Category: Stehle, T]]
	[[Category: Coat protein]]		[[Category: Coat protein]]
	[[Category: Icosahedral virus]]		[[Category: Icosahedral virus]]
	[[Category: Virus]]		[[Category: Virus]]

OCA at 20:30, 28 September 2014

OCA — Sun, 28 Sep 2014 20:30:41 GMT

←Older revision		Revision as of 20:30, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1sie.~~png~~\|~~left~~\|200px]]	+	==MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE==
		+	<StructureSection load='1sie' size='340' side='right' caption='[[1sie]], [[Resolution\|resolution]] 3.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1sie]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SIE FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sie OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sie RCSB], [http://www.ebi.ac.uk/pdbsum/1sie PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/si/1sie_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Murine polyomavirus recognizes (alpha2,3)-linked alpha-5-N-acetylneuraminic acid (sialic acid) on the surface of susceptible cells. While all strains bind to straight-chain receptors terminating in (alpha2,3)-linked sialic acid, some strains also bind to branched oligosaccharides that carry a second, (alpha2,6)-linked sialic acid. The ability to bind to these branched-chain receptors correlates with a single amino acid mutation at position 91 on the outer surface of the major capsid protein, VP1, and with a significant decrease in tumorigenicity. RESULTS: We have determined the structures of polyomavirus strain P16, which bears a glycine at position 91, in complex with model compounds for both straight-chain and branched-chain sialoglycoconjugates. The structures have been refined to a resolution of 3.65 degree. The ligands bind to a shallow groove on the surface of VP1. The sialic acid-(alpha2,3)-galactose moiety, which is common to both compounds, has specific and identical contacts. The additional (alpha2,6)-linked sialic acid moiety of the branched-chain receptor fragment fits into a surface pocket, but it has high thermal factors and does not form hydrogen bonds to groups on VP1. Data collected from crystals soaked at different oligosaccharide concentrations establish that both receptor fragments have similar, low affinities (dissociation constants in the range 5-10 mM) for the P16 virus, consistent with the interactions seen in the two complexes. CONCLUSION: The oligosaccharide-binding groove is complementary to the shape of the bound glycan, but there are relatively few hydrogen bonds between glycan and protein. Thus, the nature of the glycosidic linkages appears to be the principal determinant of specificity, rather than the position of particular hydroxyl groups. The low receptor affinity may be important for avoiding inhibition of viral release by retention on surface receptors of infected cells. Evidence suggests that strains with still greater pathogenicity are likely to have even weaker affinity.

-	~~{{STRUCTURE_1sie\| PDB=1sie \| SCENE= }}~~	+	Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments.,Stehle T, Harrison SC Structure. 1996 Feb 15;4(2):183-94. PMID:8805524<ref>PMID:8805524</ref>

-	~~===MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8805524}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1sie]] is~~ a ~~6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Viruses Viruses]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1SIE OCA].~~	+

	==See Also==		==See Also==
	*[[Virus coat protein\|Virus coat protein]]		*[[Virus coat protein\|Virus coat protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008805524<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Viruses]]		[[Category: Viruses]]
	[[Category: Harrison, S C.]]		[[Category: Harrison, S C.]]