6ieq - Revision history

OCA at 09:20, 20 March 2024

OCA — Wed, 20 Mar 2024 09:20:03 GMT

←Older revision		Revision as of 09:20, 20 March 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ieq OCA], [https://pdbe.org/6ieq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ieq RCSB], [https://www.ebi.ac.uk/pdbsum/6ieq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ieq 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=6ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ieq OCA], [https://pdbe.org/6ieq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ieq RCSB], [https://www.ebi.ac.uk/pdbsum/6ieq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ieq ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Stabilized HIV-1 envelope glycoproteins (Env) that resemble the native Env are utilized in vaccination strategies aimed at inducing broadly neutralizing antibodies (bNAbs). To limit the exposure of rare isolate-specific antigenic residues/determinants we generated a SOSIP trimer based on a consensus sequence of all HIV-1 group M isolates (ConM). The ConM trimer displays the epitopes of most known bNAbs and several germline bNAb precursors. The crystal structure of the ConM trimer at 3.9 A resolution resembles that of the native Env trimer and its antigenic surface displays few rare residues. The ConM trimer elicits strong NAb responses against the autologous virus in rabbits and macaques that are significantly enhanced when it is presented on ferritin nanoparticles. The dominant NAb specificity is directed against an epitope at or close to the trimer apex. Immunogens based on consensus sequences might have utility in engineering vaccines against HIV-1 and other viruses.
-
-	Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence.,Sliepen K, Han BW, Bontjer I, Mooij P, Garces F, Behrens AJ, Rantalainen K, Kumar S, Sarkar A, Brouwer PJM, Hua Y, Tolazzi M, Schermer E, Torres JL, Ozorowski G, van der Woude P, de la Pena AT, van Breemen MJ, Camacho-Sanchez JM, Burger JA, Medina-Ramirez M, Gonzalez N, Alcami J, LaBranche C, Scarlatti G, van Gils MJ, Crispin M, Montefiori DC, Ward AB, Koopman G, Moore JP, Shattock RJ, Bogers WM, Wilson IA, Sanders RW Nat Commun. 2019 May 29;10(1):2355. doi: 10.1038/s41467-019-10262-5. PMID:31142746<ref>PMID:31142746</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6ieq" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:40, 22 November 2023

OCA — Wed, 22 Nov 2023 09:40:08 GMT

←Older revision		Revision as of 09:40, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6ieq' size='340' side='right'caption='[[6ieq]], [[Resolution\|resolution]] 3.90Å' scene=''>		<StructureSection load='6ieq' size='340' side='right'caption='[[6ieq]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ieq]] is a 6 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=6IEQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ieq]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IEQ 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.9Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~UNK~~:~~UNKNOWN~~'>~~UNK~~</scene></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>, <scene name='pdbligand=PRD_900118:6alpha-alpha-mannobiose'>PRD_900118</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=6ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ieq OCA], [~~http~~://pdbe.org/6ieq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ieq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ieq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ieq 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=6ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ieq OCA], [https://pdbe.org/6ieq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ieq RCSB], [https://www.ebi.ac.uk/pdbsum/6ieq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ieq 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: Human]]	+	[[Category: Homo sapiens]]
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Han~~, B W~~]]	+	[[Category: Han BW]]
-	[[Category: Wilson~~, I A]]~~	+	[[Category: Wilson IA]]
-	~~[[Category: Broadly neutralizing antibody]]~~	+
-	~~[[Category: Consensus sequence-based conm sosip]]~~	+
-	~~[[Category: Envelop protein]]~~	+
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 06:13, 12 June 2019

OCA — Wed, 12 Jun 2019 06:13:58 GMT

←Older revision		Revision as of 06:13, 12 June 2019
Line 3:		Line 3:
	<StructureSection load='6ieq' size='340' side='right'caption='[[6ieq]], [[Resolution\|resolution]] 3.90Å' scene=''>		<StructureSection load='6ieq' size='340' side='right'caption='[[6ieq]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ieq]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ieq]] is a 6 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=6IEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IEQ 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=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</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=6ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ieq OCA], [http://pdbe.org/6ieq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ieq RCSB], [http://www.ebi.ac.uk/pdbsum/6ieq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ieq 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=6ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ieq OCA], [http://pdbe.org/6ieq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ieq RCSB], [http://www.ebi.ac.uk/pdbsum/6ieq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ieq ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Stabilized HIV-1 envelope glycoproteins (Env) that resemble the native Env are utilized in vaccination strategies aimed at inducing broadly neutralizing antibodies (bNAbs). To limit the exposure of rare isolate-specific antigenic residues/determinants we generated a SOSIP trimer based on a consensus sequence of all HIV-1 group M isolates (ConM). The ConM trimer displays the epitopes of most known bNAbs and several germline bNAb precursors. The crystal structure of the ConM trimer at 3.9 A resolution resembles that of the native Env trimer and its antigenic surface displays few rare residues. The ConM trimer elicits strong NAb responses against the autologous virus in rabbits and macaques that are significantly enhanced when it is presented on ferritin nanoparticles. The dominant NAb specificity is directed against an epitope at or close to the trimer apex. Immunogens based on consensus sequences might have utility in engineering vaccines against HIV-1 and other viruses.
		+
		+	Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence.,Sliepen K, Han BW, Bontjer I, Mooij P, Garces F, Behrens AJ, Rantalainen K, Kumar S, Sarkar A, Brouwer PJM, Hua Y, Tolazzi M, Schermer E, Torres JL, Ozorowski G, van der Woude P, de la Pena AT, van Breemen MJ, Camacho-Sanchez JM, Burger JA, Medina-Ramirez M, Gonzalez N, Alcami J, LaBranche C, Scarlatti G, van Gils MJ, Crispin M, Montefiori DC, Ward AB, Koopman G, Moore JP, Shattock RJ, Bogers WM, Wilson IA, Sanders RW Nat Commun. 2019 May 29;10(1):2355. doi: 10.1038/s41467-019-10262-5. PMID:31142746<ref>PMID:31142746</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ieq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Han, B W]]		[[Category: Han, B W]]

OCA at 06:50, 23 May 2019

OCA — Thu, 23 May 2019 06:50:09 GMT

←Older revision		Revision as of 06:50, 23 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ieq ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb PGT124 and 35O22==
-		+	<StructureSection load='6ieq' size='340' side='right'caption='[[6ieq]], [[Resolution\|resolution]] 3.90Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ieq]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IEQ FirstGlance]. <br>
-	~~Description~~:	+	</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>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</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=6ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ieq OCA], [http://pdbe.org/6ieq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ieq RCSB], [http://www.ebi.ac.uk/pdbsum/6ieq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ieq ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Han, B W]]
		+	[[Category: Wilson, I A]]
		+	[[Category: Broadly neutralizing antibody]]
		+	[[Category: Consensus sequence-based conm sosip]]
		+	[[Category: Envelop protein]]
		+	[[Category: Hiv-1]]
		+	[[Category: Viral protein]]

OCA at 04:47, 2 January 2019

OCA — Wed, 02 Jan 2019 04:47:20 GMT

←Older revision		Revision as of 04:47, 2 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ieq is ON HOLD	+	The entry 6ieq is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 26 Sep 2018 06:20:37 GMT

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

←Older revision

Revision as of 06:20, 26 September 2018

OCA: New page: '''Unreleased structure''' The entry 6ieq is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Sep 2018 06:20:35 GMT

New page: '''Unreleased structure''' The entry 6ieq is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ieq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]