6u50 - Revision history

OCA at 07:44, 11 October 2023

OCA — Wed, 11 Oct 2023 07:44:13 GMT

←Older revision		Revision as of 07:44, 11 October 2023
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	<StructureSection load='6u50' size='340' side='right'caption='[[6u50]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6u50' size='340' side='right'caption='[[6u50]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u50]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Camelus_glama Camelus~~ glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U50 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6U50 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u50]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U50 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U50 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 1.6Å</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=6u50 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u50 OCA], [~~http~~://pdbe.org/6u50 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6u50 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6u50 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6u50 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=6u50 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u50 OCA], [https://pdbe.org/6u50 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u50 RCSB], [https://www.ebi.ac.uk/pdbsum/6u50 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u50 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Camelus~~ glama]]	+	[[Category: Lama glama]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hart~~, P J~~]]	+	[[Category: Hart PJ]]
-	[[Category: Hayhurst, A]]	+	[[Category: Hayhurst A]]
-	[[Category: Sherwood~~, L J~~]]	+	[[Category: Sherwood LJ]]
-	[[Category: Taylor~~, A B]]~~	+	[[Category: Taylor AB]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Ebola]]~~	+
-	~~[[Category: Filovirus]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Nanobody~~]]	+

OCA at 10:57, 4 December 2019

OCA — Wed, 04 Dec 2019 10:57:17 GMT

←Older revision		Revision as of 10:57, 4 December 2019
Line 3:		Line 3:
	<StructureSection load='6u50' size='340' side='right'caption='[[6u50]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6u50' size='340' side='right'caption='[[6u50]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u50]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U50 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U50 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u50]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U50 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U50 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=6u50 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u50 OCA], [http://pdbe.org/6u50 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u50 RCSB], [http://www.ebi.ac.uk/pdbsum/6u50 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u50 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=6u50 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u50 OCA], [http://pdbe.org/6u50 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u50 RCSB], [http://www.ebi.ac.uk/pdbsum/6u50 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u50 ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Camelus glama]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hart, P J]]		[[Category: Hart, P J]]

OCA at 06:56, 6 November 2019

OCA — Wed, 06 Nov 2019 06:56:21 GMT

←Older revision		Revision as of 06:56, 6 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6u50 is ~~ON HOLD until Paper~~ Publication	+	==Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)==
		+	<StructureSection load='6u50' size='340' side='right'caption='[[6u50]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6u50]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U50 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U50 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=6u50 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u50 OCA], [http://pdbe.org/6u50 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u50 RCSB], [http://www.ebi.ac.uk/pdbsum/6u50 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u50 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We had previously shown that three anti-Marburgvirus nanobodies (VHH or sdAb) targeted a cryptotope within an alpha-helical assembly at the nucleoprotein (NP) C-terminus that was conserved through half a century of viral evolution. Here, we wished to determine whether an anti-Ebola virus sdAb, that was cross-reactive within the Ebolavirus genus, recognized a similar structural feature upstream of the ebolaviral NP C-terminus. Additionally, we sought to determine whether the specificities of a less cross-reactive anti-Zaire ebolavirus sdAb and a totally specific anti-Sudan ebolavirus sdAb were the result of exclusion from this region. Binding and X-ray crystallographic studies revealed that the primary determinant of cross-reactivity did indeed appear to be a preference for the helical feature. Specificity, in the case of the Zaire ebolavirus specific sdAb arose from the footprint shifting away from the helices, to engage more variable residues. While both sdAb employed CDRs they also had atypical side-on approaches with framework 2 (FR2) helping to accommodate parts of the epitope in sizeable paratope gullies. The Sudan ebolavirus specific sdAb was more remarkable and appeared to bind two C-terminal domains simultaneously via non-overlapping epitopes - "paratope duality". One mode involved paratope gullying, while the other involved only CDRs, with CDR3 restructuring to wedge in between opposing walls of an inter-domain crevice. The varied routes used by sdAb to engage antigen discovered here deepen our appreciation of the small scaffold's architectural versatility, and also reveal lucrative opportunities within the ebolavirus NP C-termini that might be leveraged for diagnostics and novel therapeutic targeting.

-	~~Authors: Taylor, A.B~~., Sherwood, ~~L.J.~~, Hart, P.J., ~~Hayhurst, A~~.	+	Paratope duality and gullying are among the atypical recognition mechanisms employed by a trio of nanobodies to differentiate ebolavirus nucleoproteins.,Sherwood LJ, Taylor AB, Hart PJ, Hayhurst A J Mol Biol. 2019 Oct 15. pii: S0022-2836(19)30597-2. doi:, 10.1016/j.jmb.2019.10.005. PMID:31626803<ref>PMID:31626803</ref>

-	~~Description: Anti~~-~~Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6u50" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hart, P J]]
	[[Category: Hayhurst, A]]		[[Category: Hayhurst, A]]
-	[[Category: Sherwood, L.J]]	+	[[Category: Sherwood, L J]]
-	[[Category: ~~Hart~~, ~~P.J~~]]	+	[[Category: Taylor, A B]]
-	[[Category: ~~Taylor, A.B~~]]	+	[[Category: Antibody]]
		+	[[Category: Ebola]]
		+	[[Category: Filovirus]]
		+	[[Category: Immune system]]
		+	[[Category: Nanobody]]

OCA: Protected "6u50" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2019 08:13:07 GMT

Protected "6u50" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:13, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6u50 is ON HOLD until Paper Publication Authors: Taylor, A.B., Sherwood, L.J., Hart, P.J., Hayhurst, A. Description: Anti-Sudan ebolavirus Nucleopr...

OCA — Wed, 02 Oct 2019 08:13:05 GMT

New page: '''Unreleased structure''' The entry 6u50 is ON HOLD until Paper Publication Authors: Taylor, A.B., Sherwood, L.J., Hart, P.J., Hayhurst, A. Description: Anti-Sudan ebolavirus Nucleopr...

New page

'''Unreleased structure'''

The entry 6u50 is ON HOLD until Paper Publication

Authors: Taylor, A.B., Sherwood, L.J., Hart, P.J., Hayhurst, A.

Description: Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)
[[Category: Unreleased Structures]]
[[Category: Hayhurst, A]]
[[Category: Sherwood, L.J]]
[[Category: Hart, P.J]]
[[Category: Taylor, A.B]]