6myy - Revision history

OCA at 03:00, 11 April 2020

OCA — Sat, 11 Apr 2020 03:00:25 GMT

←Older revision		Revision as of 03:00, 11 April 2020
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	<SX load='6myy' size='340' side='right' viewer='molstar' caption='[[6myy]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='6myy' size='340' side='right' viewer='molstar' caption='[[6myy]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6myy]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6myy]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6MYY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6mft\|6mft]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6mft\|6mft]]</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=6myy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myy OCA], [http://pdbe.org/6myy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6myy RCSB], [http://www.ebi.ac.uk/pdbsum/6myy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6myy ProSAT]</span></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=6myy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myy OCA], [http://pdbe.org/6myy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6myy RCSB], [http://www.ebi.ac.uk/pdbsum/6myy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6myy ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:39, 6 March 2020

OCA — Fri, 06 Mar 2020 22:39:43 GMT

←Older revision		Revision as of 22:39, 6 March 2020
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	==Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map==		==Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map==
-	<~~StructureSection~~ load='6myy' size='340' side='right'caption='[[6myy]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<SX load='6myy' size='340' side='right' viewer='molstar' caption='[[6myy]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6myy]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MYY FirstGlance]. <br>		<table><tr><td colspan='2'>[[6myy]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MYY FirstGlance]. <br>
Line 21:		Line 21:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Human]]		[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 09:08, 8 January 2020

OCA — Wed, 08 Jan 2020 09:08:01 GMT

←Older revision		Revision as of 09:08, 8 January 2020
Line 1:		Line 1:

	==Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map==		==Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map==
-	<StructureSection load='6myy' size='340' side='right' caption='[[6myy]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<StructureSection load='6myy' size='340' side='right'caption='[[6myy]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6myy]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6myy]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MYY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
Line 9:		Line 9:
	<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=6myy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myy OCA], [http://pdbe.org/6myy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6myy RCSB], [http://www.ebi.ac.uk/pdbsum/6myy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6myy 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=6myy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myy OCA], [http://pdbe.org/6myy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6myy RCSB], [http://www.ebi.ac.uk/pdbsum/6myy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6myy ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4BS) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding VRC01 germline precursors poorly bind to Env. Immunogen design has mostly relied on glycan removal from trimeric Env constructs and has had limited success in eliciting mature VRC01 bnAbs. To better understand elicitation of such bnAbs, we characterized the inferred germline precursor of VRC01 in complex with a modified trimeric 426c Env by cryo-electron microscopy and a 426c gp120 core by X-ray crystallography, biolayer interferometry, immunoprecipitation, and glycoproteomics. Our results show VRC01 germline antibodies interacted with a wild-type 426c core lacking variable loops 1-3 in the presence and absence of a glycan at position Asn276, with the latter form binding with higher affinity than the former. Interactions in the presence of an Asn276 oligosaccharide could be enhanced upon carbohydrate shortening, which should be considered for immunogen design.
		+
		+	Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core.,Borst AJ, Weidle CE, Gray MD, Frenz B, Snijder J, Joyce MG, Georgiev IS, Stewart-Jones GB, Kwong PD, McGuire AT, DiMaio F, Stamatatos L, Pancera M, Veesler D Elife. 2018 Nov 7;7. pii: 37688. doi: 10.7554/eLife.37688. PMID:30403372<ref>PMID:30403372</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6myy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Borst, A J]]		[[Category: Borst, A J]]
	[[Category: DiMaio, F]]		[[Category: DiMaio, F]]

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

OCA — Wed, 14 Nov 2018 08:24:37 GMT

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

←Older revision

Revision as of 08:24, 14 November 2018

OCA: New page: ==Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map== == Structural highlights ==
<table><tr><td colspan='2'>[[6myy]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYY OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MYY FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl">[[Non-Standard_Residue|NonStd Res:]]</td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[6mft|6mft]]</td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6myy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myy OCA], [http://pdbe.org/6myy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6myy RCSB], [http://www.ebi.ac.uk/pdbsum/6myy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6myy ProSAT]</td></tr>
</table>
TOC
</StructureSection>
[[Category: Borst, A J]]
[[Category: DiMaio, F]]
[[Category: Frenz, B]]
[[Category: Georgiev, I S]]
[[Category: Gray, M D]]
[[Category: Joyce, M G]]
[[Category: Kwong, P D]]
[[Category: McGuire, A T]]
[[Category: Pancera, M]]
[[Category: Snijder, J]]
[[Category: Stamatatos, L]]
[[Category: Stewart-Jones, G B.E]]
[[Category: Veesler, D]]
[[Category: Weidle, C E]]
[[Category: Germline vrc01 antibody]]
[[Category: Glycan shield]]
[[Category: Hiv envelope]]
[[Category: Viral fusion protein]]
[[Category: Viral protein-immune system complex]]