5omn - Revision history

OCA at 16:54, 13 December 2023

2023-12-13T16:54:49Z

←Older revision		Revision as of 16:54, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='5omn' size='340' side='right'caption='[[5omn]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='5omn' size='340' side='right'caption='[[5omn]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5omn]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Alpaca Alpaca~~] and [~~http~~://en.wikipedia.org/wiki/~~Norwalk_calicivirus Norwalk calicivirus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OMN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5omn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Norwalk_virus Norwalk virus] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OMN 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=5omn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omn OCA], [~~http~~://pdbe.org/5omn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5omn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5omn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5omn ProSAT]</span></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]] 2.682Å</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=5omn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omn OCA], [https://pdbe.org/5omn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5omn RCSB], [https://www.ebi.ac.uk/pdbsum/5omn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5omn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5F4T5_9CALI Q5F4T5_9CALI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 21:
	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]		*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
Line 23:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Alpaca]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Norwalk ~~calicivirus~~]]	+	[[Category: Norwalk virus]]
-	[[Category: ~~Hansman, G S~~]]	+	[[Category: Vicugna pacos]]
-	[[Category: ~~Koromyslova, A D~~]]	+	[[Category: Hansman GS]]
-	[[Category: ~~Capsid]]~~	+	[[Category: Koromyslova AD]]
-	~~[[Category: Nanobody]]~~	+
-	~~[[Category: Norovirus]]~~	+
-	~~[[Category: Protruding domain]]~~	+
-	~~[[Category: Vhh]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 07:29, 2 September 2020

2020-09-02T07:29:00Z

←Older revision		Revision as of 07:29, 2 September 2020
Line 1:		Line 1:

	==GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-27==		==GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-27==
-	<StructureSection load='5omn' size='340' side='right' caption='[[5omn]], [[Resolution\|resolution]] 2.68Å' scene=''>	+	<StructureSection load='5omn' size='340' side='right'caption='[[5omn]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5omn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alpaca Alpaca] and [http://en.wikipedia.org/wiki/Norwalk_calicivirus Norwalk calicivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMN OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OMN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5omn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alpaca Alpaca] and [http://en.wikipedia.org/wiki/Norwalk_calicivirus Norwalk calicivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OMN FirstGlance]. <br>
-	</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=5omn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omn OCA], [http://pdbe.org/5omn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omn RCSB], [http://www.ebi.ac.uk/pdbsum/5omn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omn ProSAT]</span></td></tr>	+	</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=5omn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omn OCA], [http://pdbe.org/5omn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omn RCSB], [http://www.ebi.ac.uk/pdbsum/5omn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	</div>		</div>
	<div class="pdbe-citations 5omn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5omn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
Line 20:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Alpaca]]		[[Category: Alpaca]]
		+	[[Category: Large Structures]]
	[[Category: Norwalk calicivirus]]		[[Category: Norwalk calicivirus]]
	[[Category: Hansman, G S]]		[[Category: Hansman, G S]]

OCA at 10:14, 15 November 2017

2017-11-15T10:14:00Z

←Older revision		Revision as of 10:14, 15 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5omn is ~~ON HOLD until Paper~~ Publication	+	==GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-27==
		+	<StructureSection load='5omn' size='340' side='right' caption='[[5omn]], [[Resolution\|resolution]] 2.68Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5omn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alpaca Alpaca] and [http://en.wikipedia.org/wiki/Norwalk_calicivirus Norwalk calicivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OMN FirstGlance]. <br>
		+	</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=5omn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omn OCA], [http://pdbe.org/5omn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omn RCSB], [http://www.ebi.ac.uk/pdbsum/5omn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omn ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Norovirus is the leading cause of gastroenteritis worldwide. Despite recent developments in norovirus propagation in cell culture, these viruses are still challenging to grow routinely. Moreover, little is known on how norovirus infects the host cells, except that histo-blood group antigens (HBGAs) are important binding factors for infection and cell entry. Antibodies that bind at the HBGA pocket and block attachment to HBGAs are believed to neutralize the virus. However, additional neutralization epitopes elsewhere on the capsid likely exist and impeding the intrinsic structural dynamics of the capsid could be equally important. In the current study, we investigated a panel of Nanobodies in order to probe functional epitopes that could trigger capsid rearrangement and/ or interfere with HBGA binding interactions. The precise binding sites of six Nanobodies (Nano-4, Nano-14, Nano-26, Nano-27, Nano-32, and Nano-42) were identified using X-ray crystallography. We showed that these Nanobodies bound on the top, side, and bottom of the norovirus protruding domain. The impact of Nanobody binding on norovirus capsid morphology was analyzed using electron microscopy and dynamic light scattering. We discovered that distinct Nanobody epitopes were associated with varied changes in particle structural integrity and assembly. Interestingly, certain Nanobody-induced capsid morphological changes lead to the capsid protein degradation and viral RNA exposure. Moreover, Nanobodies employed multiple inhibition mechanisms to prevent norovirus attachment to HBGAs, which included steric obstruction (Nano-14), allosteric interference (Nano-32), and violation of normal capsid morphology (Nano-26 and Nano-85). Finally, we showed that two Nanobodies (Nano-26 and Nano-85) not only compromised capsid integrity and inhibited VLPs attachment to HBGAs, but also recognized a broad panel of norovirus genotypes with high affinities. Consequently, Nano-26 and Nano-85 have a great potential to function as novel therapeutic agents against human noroviruses.

-	~~Authors:~~ Koromyslova, A.D.~~, Hansman, G~~.S.	+	Nanobodies targeting norovirus capsid reveal functional epitopes and potential mechanisms of neutralization.,Koromyslova AD, Hansman GS PLoS Pathog. 2017 Nov 2;13(11):e1006636. doi: 10.1371/journal.ppat.1006636., eCollection 2017 Nov. PMID:29095961<ref>PMID:29095961</ref>

-	~~Description: GII~~.~~10 Vietnam 026 protruding domain in complex with Nanobody Nano~~-27	+	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 5omn" style="background-color:#fffaf0;"></div>
-	[[Category: Hansman, G.S]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alpaca]]
		+	[[Category: Norwalk calicivirus]]
		+	[[Category: Hansman, G S]]
		+	[[Category: Koromyslova, A D]]
		+	[[Category: Capsid]]
		+	[[Category: Nanobody]]
		+	[[Category: Norovirus]]
		+	[[Category: Protruding domain]]
		+	[[Category: Vhh]]
		+	[[Category: Viral protein]]

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

2017-09-27T12:35:59Z

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

←Older revision

Revision as of 12:35, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5omn is ON HOLD until Paper Publication Authors: Koromyslova, A.D., Hansman, G.S. Description: GII.10 Vietnam 026 protruding domain in complex with...

2017-09-27T12:35:58Z

New page: '''Unreleased structure''' The entry 5omn is ON HOLD until Paper Publication Authors: Koromyslova, A.D., Hansman, G.S. Description: GII.10 Vietnam 026 protruding domain in complex with...

New page

'''Unreleased structure'''

The entry 5omn is ON HOLD until Paper Publication

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

Description: GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-27
[[Category: Unreleased Structures]]
[[Category: Koromyslova, A.D]]
[[Category: Hansman, G.S]]