4x1w - Revision history

OCA at 10:46, 10 January 2024

2024-01-10T10:46:08Z

←Older revision		Revision as of 10:46, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x1w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rabbit_hemorrhagic_disease_virus Rabbit hemorrhagic disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X1W FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x1w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rabbit_hemorrhagic_disease_virus Rabbit hemorrhagic disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X1W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.95Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=4x1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1w OCA], [https://pdbe.org/4x1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x1w RCSB], [https://www.ebi.ac.uk/pdbsum/4x1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1w 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=4x1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1w OCA], [https://pdbe.org/4x1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x1w RCSB], [https://www.ebi.ac.uk/pdbsum/4x1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1w ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:07, 12 April 2023

2023-04-12T21:07:14Z

←Older revision		Revision as of 21:07, 12 April 2023
Line 3:		Line 3:
	<StructureSection load='4x1w' size='340' side='right'caption='[[4x1w]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='4x1w' size='340' side='right'caption='[[4x1w]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x1w]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhdv Rhdv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4X1W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x1w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rabbit_hemorrhagic_disease_virus Rabbit hemorrhagic disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X1W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=11976 RHDV])~~</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=4x1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1w OCA], [https://pdbe.org/4x1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x1w RCSB], [https://www.ebi.ac.uk/pdbsum/4x1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1w 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=4x1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1w OCA], [~~http~~://pdbe.org/4x1w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4x1w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4x1w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1w ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/I7FLU3_RHDV I7FLU3_RHDV]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4x1w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4x1w" 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: ~~Rhdv~~]]	+	[[Category: Rabbit hemorrhagic disease virus]]
-	[[Category: Hansman~~, G S~~]]	+	[[Category: Hansman GS]]
-	[[Category: Leuthold~~, M M]]~~	+	[[Category: Leuthold MM]]
-	~~[[Category: Capsid spike]]~~	+
-	~~[[Category: Dimer]]~~	+
-	~~[[Category: Hbga binding]]~~	+
-	~~[[Category: Major capsid protein]]~~	+
-	~~[[Category: Protruding domain]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 08:36, 23 May 2019

2019-05-23T08:36:40Z

←Older revision		Revision as of 08:36, 23 May 2019
Line 1:		Line 1:
		+
	==Crystal structure of unbound RHDVb P domain==		==Crystal structure of unbound RHDVb P domain==
-	<StructureSection load='4x1w' size='340' side='right' caption='[[4x1w]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='4x1w' size='340' side='right'caption='[[4x1w]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x1w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X1W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x1w]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhdv Rhdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X1W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=4x1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1w OCA], [http://pdbe.org/4x1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x1w RCSB], [http://www.ebi.ac.uk/pdbsum/4x1w PDBsum]</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=11976 RHDV])</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=4x1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1w OCA], [http://pdbe.org/4x1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x1w RCSB], [http://www.ebi.ac.uk/pdbsum/4x1w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1w ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Rhdv]]
	[[Category: Hansman, G S]]		[[Category: Hansman, G S]]
	[[Category: Leuthold, M M]]		[[Category: Leuthold, M M]]

OCA at 07:26, 7 October 2015

2015-10-07T07:26:28Z

←Older revision		Revision as of 07:26, 7 October 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[4x1w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X1W FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x1w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X1W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=4x1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x1w RCSB], [http://www.ebi.ac.uk/pdbsum/4x1w 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=4x1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1w OCA], [http://pdbe.org/4x1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x1w RCSB], [http://www.ebi.ac.uk/pdbsum/4x1w PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	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 4x1w" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:27, 14 January 2015

2015-01-14T13:27:35Z

←Older revision		Revision as of 13:27, 14 January 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of unbound RHDVb P domain==
		+	<StructureSection load='4x1w' size='340' side='right' caption='[[4x1w]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4x1w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X1W FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=4x1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x1w RCSB], [http://www.ebi.ac.uk/pdbsum/4x1w PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Rabbit hemorrhagic disease virus (RHDV) is a member of the Caliciviridae family (Lagovirus genus). RHDV is highly contagious and attaches to epithelial cells in the digestive or respiratory tract, leading to massive lesions with high mortality rates. A new variant of RHDV (termed RHDVb) has recently emerged and previously vaccinated rabbits appear to have little protection against this new strain. Similar to human norovirus (Caliciviridae, Norovirus genus), RHDV binds histo-blood group antigens (HBGAs) and this is thought to be important for infection. Here, we report the HBGA binding site on the RHDVb capsid-protruding domain (P domain) using X-ray crystallography. The HBGA binding pocket was located in a negatively charged patch on the side of the P domain and at a dimeric interface. Residues from both monomers contributed to the HBGA binding and involved a network of direct hydrogen bonds and water-mediated interactions. An amino acid sequence alignment of different RHDV strains indicated that the residues directly interacting with the ABH-fucose of the HBGAs (Asp472, Asn474, and Ser479) were highly conserved. This result suggested that different RHDV strains could also bind HBGAs at the equivalent pocket. Moreover, several HBGA binding characteristics between RHDVb and human genogroup II norovirus were similar, which indicated a possible convergent evolution of HBGA binding interactions. Further structural studies with other RHDV strains are needed in order to better understand the HBGA binding mechanisms among the diverse RHDV strains. IMPORTANCE: We identified, for the first time, the HBGA binding site on an RHDVb P domain using X-ray crystallography. Our results showed that RHDVb and human genogroup II noroviruses had similar HBGA binding interactions. Recently, it was discovered that synthetic HBGAs or HBGA-expressing enteric bacteria could enhance human genogroup II norovirus infection in B cells. Considering that RHDVb and genogroup II norovirus similarly interacted with HBGAs, it may be possible that a comparable cell culture system could also work with RHDVb. Taken together, these new findings will extend our understanding of calicivirus HBGA interactions and may help to elucidate the specific roles of HBGAs in calicivirus infections.

-	~~The entry 4x1w is ON HOLD~~	+	Structural Analysis of a Rabbit Hemorrhagic Disease Virus Binding to Histo-Blood Group Antigens.,Leuthold MM, Dalton KP, Hansman GS J Virol. 2014 Dec 10. pii: JVI.02832-14. PMID:25505081<ref>PMID:25505081</ref>

-	~~Authors: Leuthold~~, ~~M.M., Hansman, G~~.S.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of variant RHDV P domain~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: Leuthold, M.M]]	+	__TOC__
-	[[Category: ~~Hansman, G.S~~]]	+	</StructureSection>
		+	[[Category: Hansman, G S]]
		+	[[Category: Leuthold, M M]]
		+	[[Category: Capsid spike]]
		+	[[Category: Dimer]]
		+	[[Category: Hbga binding]]
		+	[[Category: Major capsid protein]]
		+	[[Category: Protruding domain]]
		+	[[Category: Viral protein]]

OCA at 20:20, 24 December 2014

2014-12-24T20:20:58Z

←Older revision		Revision as of 20:20, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of variant RHDV P domain		Description: Crystal structure of variant RHDV P domain
		+	[[Category: Unreleased Structures]]
		+	[[Category: Leuthold, M.M]]
		+	[[Category: Hansman, G.S]]

OCA: Protected "4x1w" [edit=sysop:move=sysop]

2014-12-03T08:46:04Z

Protected "4x1w" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:46, 3 December 2014

OCA: New page: '''Unreleased structure''' The entry 4x1w is ON HOLD Authors: Leuthold, M.M., Hansman, G.S. Description: Crystal structure of variant RHDV P domain

2014-12-03T08:46:02Z

New page: '''Unreleased structure''' The entry 4x1w is ON HOLD Authors: Leuthold, M.M., Hansman, G.S. Description: Crystal structure of variant RHDV P domain

New page

'''Unreleased structure'''

The entry 4x1w is ON HOLD

Authors: Leuthold, M.M., Hansman, G.S.

Description: Crystal structure of variant RHDV P domain