5n7m - Revision history

OCA at 12:32, 15 November 2023

2023-11-15T12:32:06Z

←Older revision		Revision as of 12:32, 15 November 2023
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	<StructureSection load='5n7m' size='340' side='right'caption='[[5n7m]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='5n7m' size='340' side='right'caption='[[5n7m]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n7m]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Hu/nv/nv~~/1968/us Hu~~/nv/nv~~/1968/us]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N7M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5N7M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n7m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Norovirus_Hu/1968/US Norovirus Hu/1968/US]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N7M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N7M 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=~~GLC~~:ALPHA-D-~~GLUCOSE~~'>~~GLC~~</scene>, <scene name='pdbligand=NA:~~SODIUM+ION~~'>NA</scene>, <scene name='pdbligand=~~FUC~~:ALPHA-L-~~FUCOSE~~'>~~FUC~~</scene>, <scene name='pdbligand=~~GAL~~:~~BETA-D-GALACTOSE~~'>~~GAL~~</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]] 1.73Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ORF2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=524364 Hu/NV/NV/1968/US])~~</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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5n7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n7m OCA], [~~http~~://pdbe.org/5n7m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5n7m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5n7m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5n7m 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=5n7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n7m OCA], [https://pdbe.org/5n7m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n7m RCSB], [https://www.ebi.ac.uk/pdbsum/5n7m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n7m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CAPSD_NVN68 CAPSD_NVN68]] Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells.<ref>PMID:16840313</ref> Soluble capsid protein may play a role in viral immunoevasion.<ref>PMID:16840313</ref>	+	[https://www.uniprot.org/uniprot/CAPSD_NVN68 CAPSD_NVN68] Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells.<ref>PMID:16840313</ref> Soluble capsid protein may play a role in viral immunoevasion.<ref>PMID:16840313</ref>
	<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 5n7m" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5n7m" 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: Hu/nv/nv/1968/us]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Hansman, G S]]~~	+	[[Category: Norovirus Hu/1968/US]]
-	~~[[Category: Koromyslova, A D]]~~	+	[[Category: Hansman GS]]
-	~~[[Category: Human milk oligosaccharide]]~~	+	[[Category: Koromyslova AD]]
-	[[Category: Norovirus]]	+
-	[[Category: ~~Protruding domain~~]]	+
-	[[Category: ~~Viral protein~~]]	+

OCA at 11:58, 26 August 2020

2020-08-26T11:58:28Z

←Older revision		Revision as of 11:58, 26 August 2020
Line 1:		Line 1:

	==Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL)==		==Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL)==
-	<StructureSection load='5n7m' size='340' side='right' caption='[[5n7m]], [[Resolution\|resolution]] 1.73Å' scene=''>	+	<StructureSection load='5n7m' size='340' side='right'caption='[[5n7m]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n7m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N7M OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5N7M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n7m]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hu/nv/nv/1968/us Hu/nv/nv/1968/us]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N7M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5N7M 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=~~FUC~~:ALPHA-L-~~FUCOSE~~'>~~FUC~~</scene>, <scene name='pdbligand=~~GAL~~:~~BETA-D-GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=~~GLC~~:ALPHA-D-~~GLUCOSE~~'>~~GLC~~</scene>, <scene name='pdbligand=NA:~~SODIUM+ION~~'>NA</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</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=5n7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n7m OCA], [http://pdbe.org/5n7m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n7m RCSB], [http://www.ebi.ac.uk/pdbsum/5n7m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n7m ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ORF2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=524364 Hu/NV/NV/1968/US])</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=5n7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n7m OCA], [http://pdbe.org/5n7m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n7m RCSB], [http://www.ebi.ac.uk/pdbsum/5n7m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n7m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hu/nv/nv/1968/us]]
		+	[[Category: Large Structures]]
	[[Category: Hansman, G S]]		[[Category: Hansman, G S]]
	[[Category: Koromyslova, A D]]		[[Category: Koromyslova, A D]]

OCA at 13:39, 24 May 2017

2017-05-24T13:39:43Z

←Older revision		Revision as of 13:39, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5n7m is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL)==
		+	<StructureSection load='5n7m' size='340' side='right' caption='[[5n7m]], [[Resolution\|resolution]] 1.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5n7m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N7M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N7M 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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5n7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n7m OCA], [http://pdbe.org/5n7m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n7m RCSB], [http://www.ebi.ac.uk/pdbsum/5n7m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n7m ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAPSD_NVN68 CAPSD_NVN68]] Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells.<ref>PMID:16840313</ref> Soluble capsid protein may play a role in viral immunoevasion.<ref>PMID:16840313</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human noroviruses are the leading cause of outbreaks of acute gastroenteritis. Norovirus interactions with histo-blood group antigens (HBGAs) are known to be important for an infection. In this study, we identified the HBGA binding pocket for an emerging GII genotype 17 (GII.17) variant using X-ray crystallography. The GII.17 variant bound the HBGA with an equivalent set of residues as the leading pandemic GII.4 variants. These structural data highlights the conserved nature of HBGA binding site between prevalent GII noroviruses. Noroviruses also interact with human milk oligosaccharides (HMOs), which mimic HBGAs and may function as receptor decoys. We previously showed that HMOs inhibited the binding of rarely detected GII.10 norovirus to HBGAs. We now found that an HMO, 2'-fucosyllactose (2'FL), additionally blocked both the GI.1 and GII.17 noroviruses from binding to HBGAs. Together, these findings provide evidence that 2'FL might function as a broadly reactive antiviral against multiple norovirus genogroups.

-	~~Authors: Hansman, G.S~~., Koromyslova, A.D.	+	Human norovirus inhibition by a human milk oligosaccharide.,Koromyslova A, Tripathi S, Morozov V, Schroten H, Hansman GS Virology. 2017 May 12;508:81-89. doi: 10.1016/j.virol.2017.04.032. PMID:28505592<ref>PMID:28505592</ref>

-	~~Description: Protruding domain~~ of GI.~~1 norovirus in complex with 2~~-~~fucosyllactose (2FL)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Koromyslova, A.D]]	+	<div class="pdbe-citations 5n7m" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Hansman, G.S~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hansman, G S]]
		+	[[Category: Koromyslova, A D]]
		+	[[Category: Human milk oligosaccharide]]
		+	[[Category: Norovirus]]
		+	[[Category: Protruding domain]]
		+	[[Category: Viral protein]]

OCA at 09:45, 5 April 2017

2017-04-05T09:45:55Z

←Older revision		Revision as of 09:45, 5 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5n7m is ON HOLD	+	The entry 5n7m is ON HOLD until Paper Publication

	Authors: Hansman, G.S., Koromyslova, A.D.		Authors: Hansman, G.S., Koromyslova, A.D.

OCA: Protected "5n7m" [edit=sysop:move=sysop]

2017-03-09T12:13:27Z

Protected "5n7m" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:13, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5n7m is ON HOLD Authors: Hansman, G.S., Koromyslova, A.D. Description: Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL) [...

2017-03-09T12:13:26Z

New page: '''Unreleased structure''' The entry 5n7m is ON HOLD Authors: Hansman, G.S., Koromyslova, A.D. Description: Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL) [...

New page

'''Unreleased structure'''

The entry 5n7m is ON HOLD

Authors: Hansman, G.S., Koromyslova, A.D.

Description: Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL)
[[Category: Unreleased Structures]]
[[Category: Koromyslova, A.D]]
[[Category: Hansman, G.S]]