4x06 - Revision history

OCA at 11:28, 9 May 2024

OCA — Thu, 09 May 2024 11:28:45 GMT

←Older revision		Revision as of 11:28, 9 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x06]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Norovirus_Hu/GII-4/Saga4/2006/JP Norovirus Hu/GII-4/Saga4/2006/JP]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X06 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x06]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Norovirus_Hu/GII-4/Saga4/2006/JP Norovirus Hu/GII-4/Saga4/2006/JP]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X06 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</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]] 1.218Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</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=4x06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x06 OCA], [https://pdbe.org/4x06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x06 RCSB], [https://www.ebi.ac.uk/pdbsum/4x06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x06 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=4x06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x06 OCA], [https://pdbe.org/4x06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x06 RCSB], [https://www.ebi.ac.uk/pdbsum/4x06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x06 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:05, 12 April 2023

OCA — Wed, 12 Apr 2023 21:05:32 GMT

←Older revision		Revision as of 21:05, 12 April 2023
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	<StructureSection load='4x06' size='340' side='right'caption='[[4x06]], [[Resolution\|resolution]] 1.22Å' scene=''>		<StructureSection load='4x06' size='340' side='right'caption='[[4x06]], [[Resolution\|resolution]] 1.22Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x06]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Norovirus_hu~~/~~gii~~-4/~~saga4~~/2006/jp Norovirus hu/~~gii~~-4/~~saga4~~/2006/jp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X06 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4X06 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x06]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Norovirus_Hu/GII-4/Saga4/2006/JP Norovirus Hu/GII-4/Saga4/2006/JP]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X06 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oox\|4oox]], [[4wzk\|4wzk]], [[4wze\|4wze]], [[4wzl\|4wzl]]~~</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=4x06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x06 OCA], [https://pdbe.org/4x06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x06 RCSB], [https://www.ebi.ac.uk/pdbsum/4x06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x06 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=4x06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x06 OCA], [~~http~~://pdbe.org/4x06 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4x06 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4x06 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4x06 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B5BTR7_9CALI B5BTR7_9CALI]
	<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 4x06" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4x06" 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: Norovirus hu/~~gii~~-4/~~saga4~~/2006/jp]]	+	[[Category: Norovirus Hu/GII-4/Saga4/2006/JP]]
-	[[Category: Hansman~~, G S~~]]	+	[[Category: Hansman GS]]
-	[[Category: Singh~~, B K]]~~	+	[[Category: Singh BK]]
-	~~[[Category: Protruding domain]]~~	+
-	~~[[Category: Viral capsid protein]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 08:52, 23 May 2019

OCA — Thu, 23 May 2019 08:52:43 GMT

←Older revision		Revision as of 08:52, 23 May 2019
Line 1:		Line 1:

	==Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type B (triglycan)==		==Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type B (triglycan)==
-	<StructureSection load='4x06' size='340' side='right' caption='[[4x06]], [[Resolution\|resolution]] 1.22Å' scene=''>	+	<StructureSection load='4x06' size='340' side='right'caption='[[4x06]], [[Resolution\|resolution]] 1.22Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x06]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X06 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x06]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Norovirus_hu/gii-4/saga4/2006/jp Norovirus hu/gii-4/saga4/2006/jp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X06 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oox\|4oox]], [[4wzk\|4wzk]], [[4wze\|4wze]], [[4wzl\|4wzl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oox\|4oox]], [[4wzk\|4wzk]], [[4wze\|4wze]], [[4wzl\|4wzl]]</td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Norovirus hu/gii-4/saga4/2006/jp]]
	[[Category: Hansman, G S]]		[[Category: Hansman, G S]]
	[[Category: Singh, B K]]		[[Category: Singh, B K]]

OCA at 00:17, 26 January 2017

OCA — Thu, 26 Jan 2017 00:17:26 GMT

←Older revision		Revision as of 00:17, 26 January 2017
Line 1:		Line 1:
		+
	==Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type B (triglycan)==		==Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type B (triglycan)==
	<StructureSection load='4x06' size='340' side='right' caption='[[4x06]], [[Resolution\|resolution]] 1.22Å' scene=''>		<StructureSection load='4x06' size='340' side='right' caption='[[4x06]], [[Resolution\|resolution]] 1.22Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oox\|4oox]], [[4wzk\|4wzk]], [[4wze\|4wze]], [[4wzl\|4wzl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oox\|4oox]], [[4wzk\|4wzk]], [[4wze\|4wze]], [[4wzl\|4wzl]]</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=4x06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x06 RCSB], [http://www.ebi.ac.uk/pdbsum/4x06 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=4x06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x06 OCA], [http://pdbe.org/4x06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x06 RCSB], [http://www.ebi.ac.uk/pdbsum/4x06 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x06 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 4x06" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:48, 17 December 2014

OCA — Wed, 17 Dec 2014 12:48:22 GMT

←Older revision		Revision as of 12:48, 17 December 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type B (triglycan)==
		+	<StructureSection load='4x06' size='340' side='right' caption='[[4x06]], [[Resolution\|resolution]] 1.22Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4x06]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X06 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oox\|4oox]], [[4wzk\|4wzk]], [[4wze\|4wze]], [[4wzl\|4wzl]]</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=4x06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x06 RCSB], [http://www.ebi.ac.uk/pdbsum/4x06 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human noroviruses are the dominant cause of outbreaks of gastroenteritis around the world. Human norovirus interacts with the polymorphic human histo-blood group antigens (HBGAs) and this interaction is thought to be important for infection. Indeed, synthetic HBGAs or HBGA-expressing enteric bacteria were shown to enhance norovirus infection in B cells. A number of studies have found a possible relationship between HBGA type and norovirus susceptibility. The genogroup II genotype 4 (GII.4) noroviruses are the dominant cluster, evolve every other year, and are thought to modify their binding interactions to different HBGA types. Here, we show the high-resolution X-ray crystal structures of the capsid protruding (P) domains from epidemic GII.4 variants in 2004, 2006, and 2012, co-crystallized with a panel of HBGA types (H type 2, Lewis Y, Lewis B, Lewis A, Lewis X, A-type, and B-type). Many of the HBGA binding interactions were found to be complex, involving capsid loop movements, alternative HBGA conformations, and HBGA rotations. We showed that a loop (residues 391-395) was elegantly repositioned in order to allow for Lewis Y binding. This loop was also slightly shifted to provide direct hydrogen and water-mediated bonds with Lewis B. We considered that the flexible loop modulated Lewis HBGA binding. The GII.4 noroviruses have dominated outbreaks over the past decade, which may be explained by their exquisite HBGA binding mechanisms, their fondness for Lewis HBGAs, and their temporal amino acid modifications. IMPORTANCE: Our data provides a comprehensive picture of GII.4 P domain and HBGA binding interactions. The exceptionally high resolutions of our X-ray crystal structures allowed us to accurately recognize novel GII.4 P domain interactions with numerous HBGA types. We showed that the GII.4 P domain HBGA interactions involved complex binding mechanisms that were not previously observed in norovirus structural studies. Many of the GII.4 P domain HBGA interactions we identified were negative in earlier ELISA-based studies. Altogether, we showed that the GII.4 norovirus P domains could accommodate numerous HBGA types.

-	~~The entry 4x06 is ON HOLD~~	+	Human Noroviruses' Fondness of Histo-Blood Group Antigens.,Singh BK, Leuthold MM, Hansman GS J Virol. 2014 Nov 26. pii: JVI.02968-14. PMID:25428879<ref>PMID:25428879</ref>

-	~~Authors: Singh~~, B.K., Hansman, G.S.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of P~~ domain ~~from norovirus strain Saga4 in complex with HBGA type B (triglycan)~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hansman, G S]]
		+	[[Category: Singh, B K]]
		+	[[Category: Protruding domain]]
		+	[[Category: Viral capsid protein]]
		+	[[Category: Viral protein]]

OCA: Protected "4x06" [edit=sysop:move=sysop]

OCA — Wed, 26 Nov 2014 07:15:30 GMT

Protected "4x06" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:15, 26 November 2014

OCA: New page: '''Unreleased structure''' The entry 4x06 is ON HOLD Authors: Singh, B.K., Hansman, G.S. Description: Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA typ...

OCA — Wed, 26 Nov 2014 07:15:29 GMT

New page: '''Unreleased structure''' The entry 4x06 is ON HOLD Authors: Singh, B.K., Hansman, G.S. Description: Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA typ...

New page

'''Unreleased structure'''

The entry 4x06 is ON HOLD

Authors: Singh, B.K., Hansman, G.S.

Description: Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type B (triglycan)