3idm - Revision history

OCA at 09:02, 15 November 2023

OCA — Wed, 15 Nov 2023 09:02:23 GMT

←Older revision		Revision as of 09:02, 15 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3idm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IDM FirstGlance]. <br>		<table><tr><td colspan='2'>[[3idm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IDM FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=NRG:N~~-~~OMEGA-NITRO-L-ARGININE'>NRG</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]] 2.24Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3d0l\|3d0l]], [[2p8m\|2p8m]], [[3idi\|3idi]], [[3idj\|3idj]], [[3idg\|3idg]], [[3idn\|3idn]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NRG:N-OMEGA-NITRO-L-ARGININE'>NRG</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=3idm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idm OCA], [https://pdbe.org/3idm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3idm RCSB], [https://www.ebi.ac.uk/pdbsum/3idm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3idm 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=3idm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idm OCA], [https://pdbe.org/3idm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3idm RCSB], [https://www.ebi.ac.uk/pdbsum/3idm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3idm ProSAT]</span></td></tr>
	</table>		</table>
Line 36:		Line 36:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bryson, S]]	+	[[Category: Bryson S]]
-	[[Category: Julien, J P]]	+	[[Category: Julien J-P]]
-	[[Category: Pai~~, E F]]~~	+	[[Category: Pai EF]]
-	~~[[Category: Gp41]]~~	+
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Mper~~]]	+

OCA at 03:30, 21 April 2022

OCA — Thu, 21 Apr 2022 03:30:03 GMT

←Older revision		Revision as of 03:30, 21 April 2022
Line 3:		Line 3:
	<StructureSection load='3idm' size='340' side='right'caption='[[3idm]], [[Resolution\|resolution]] 2.24Å' scene=''>		<StructureSection load='3idm' size='340' side='right'caption='[[3idm]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3idm]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IDM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3idm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IDM FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NRG:N-OMEGA-NITRO-L-ARGININE'>NRG</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NRG:N-OMEGA-NITRO-L-ARGININE'>NRG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d0l\|3d0l]], [[2p8m\|2p8m]], [[3idi\|3idi]], [[3idj\|3idj]], [[3idg\|3idg]], [[3idn\|3idn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3d0l\|3d0l]], [[2p8m\|2p8m]], [[3idi\|3idi]], [[3idj\|3idj]], [[3idg\|3idg]], [[3idn\|3idn]]</div></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=3idm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idm OCA], [~~http~~://pdbe.org/3idm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3idm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3idm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3idm 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=3idm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idm OCA], [https://pdbe.org/3idm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3idm RCSB], [https://www.ebi.ac.uk/pdbsum/3idm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3idm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:17, 7 August 2019

OCA — Wed, 07 Aug 2019 07:17:52 GMT

←Older revision		Revision as of 07:17, 7 August 2019
Line 1:		Line 1:

	==Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS==		==Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS==
-	<StructureSection load='3idm' size='340' side='right' caption='[[3idm]], [[Resolution\|resolution]] 2.24Å' scene=''>	+	<StructureSection load='3idm' size='340' side='right'caption='[[3idm]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3idm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IDM FirstGlance]. <br>		<table><tr><td colspan='2'>[[3idm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IDM FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/id/3idm_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/id/3idm_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 29:		Line 29:

	==See Also==		==See Also==
-	*[[3D structures ~~of monoclonal antibody~~\|3D structures ~~of monoclonal antibody~~]]	+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
	[[Category: Bryson, S]]		[[Category: Bryson, S]]
	[[Category: Julien, J P]]		[[Category: Julien, J P]]

OCA at 16:41, 11 August 2016

OCA — Thu, 11 Aug 2016 16:41:01 GMT

←Older revision		Revision as of 16:41, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS==		==Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS==
	<StructureSection load='3idm' size='340' side='right' caption='[[3idm]], [[Resolution\|resolution]] 2.24Å' scene=''>		<StructureSection load='3idm' size='340' side='right' caption='[[3idm]], [[Resolution\|resolution]] 2.24Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NRG:N-OMEGA-NITRO-L-ARGININE'>NRG</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NRG:N-OMEGA-NITRO-L-ARGININE'>NRG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d0l\|3d0l]], [[2p8m\|2p8m]], [[3idi\|3idi]], [[3idj\|3idj]], [[3idg\|3idg]], [[3idn\|3idn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d0l\|3d0l]], [[2p8m\|2p8m]], [[3idi\|3idi]], [[3idj\|3idj]], [[3idg\|3idg]], [[3idn\|3idn]]</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=3idm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3idm RCSB], [http://www.ebi.ac.uk/pdbsum/3idm 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=3idm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idm OCA], [http://pdbe.org/3idm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3idm RCSB], [http://www.ebi.ac.uk/pdbsum/3idm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3idm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3idm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 26:
	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 3idm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[~~Monoclonal Antibody~~\|~~Monoclonal Antibody~~]]	+	*[[3D structures of monoclonal antibody\|3D structures of monoclonal antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:53, 20 January 2015

OCA — Tue, 20 Jan 2015 10:53:16 GMT

←Older revision		Revision as of 10:53, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3idm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IDM FirstGlance]. <br>		<table><tr><td colspan='2'>[[3idm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IDM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NRG:N-OMEGA-NITRO-L-ARGININE'>NRG</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NRG:N-OMEGA-NITRO-L-ARGININE'>NRG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d0l\|3d0l]], [[2p8m\|2p8m]], [[3idi\|3idi]], [[3idj\|3idj]], [[3idg\|3idg]], [[3idn\|3idn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d0l\|3d0l]], [[2p8m\|2p8m]], [[3idi\|3idi]], [[3idj\|3idj]], [[3idg\|3idg]], [[3idn\|3idn]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3idm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3idm RCSB], [http://www.ebi.ac.uk/pdbsum/3idm 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=3idm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3idm RCSB], [http://www.ebi.ac.uk/pdbsum/3idm PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Bryson, S.]]	+	[[Category: Bryson, S]]
-	[[Category: Julien, J P.]]	+	[[Category: Julien, J P]]
-	[[Category: Pai, E F~~.]]~~	+	[[Category: Pai, E F]]
-	~~[[Category: 2f5~~]]	+
	[[Category: Gp41]]		[[Category: Gp41]]
	[[Category: Hiv-1]]		[[Category: Hiv-1]]
	[[Category: Immune system]]		[[Category: Immune system]]
	[[Category: Mper]]		[[Category: Mper]]

OCA at 12:39, 29 September 2014

OCA — Mon, 29 Sep 2014 12:39:35 GMT

←Older revision		Revision as of 12:39, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3idm.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS==
		+	<StructureSection load='3idm' size='340' side='right' caption='[[3idm]], [[Resolution\|resolution]] 2.24Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3idm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IDM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NRG:N-OMEGA-NITRO-L-ARGININE'>NRG</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d0l\|3d0l]], [[2p8m\|2p8m]], [[3idi\|3idi]], [[3idj\|3idj]], [[3idg\|3idg]], [[3idn\|3idn]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3idm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3idm RCSB], [http://www.ebi.ac.uk/pdbsum/3idm PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/id/3idm_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The quest to create a human immunodeficiency virus type 1 (HIV-1) vaccine capable of eliciting broadly neutralizing antibodies against Env has been challenging. Among other problems, one difficulty in creating a potent immunogen resides in the substantial overall sequence variability of the HIV envelope protein. The membrane-proximal region (MPER) of gp41 is a particularly conserved tryptophan-rich region spanning residues 659 to 683, which is recognized by three broadly neutralizing monoclonal antibodies (bnMAbs), 2F5, Z13, and 4E10. In this study, we first describe the variability of residues in the gp41 MPER and report on the invariant nature of 15 out of 25 amino acids comprising this region. Subsequently, we evaluate the ability of the bnMAb 2F5 to recognize 31 varying sequences of the gp41 MPER at a molecular level. In 19 cases, resulting crystal structures show the various MPER peptides bound to the 2F5 Fab'. A variety of amino acid substitutions outside the 664DKW666 core epitope are tolerated. However, changes at the 664DKW666 motif itself are restricted to those residues that preserve the aspartate's negative charge, the hydrophobic alkyl-pi stacking arrangement between the beta-turn lysine and tryptophan, and the positive charge of the former. We also characterize a possible molecular mechanism of 2F5 escape by sequence variability at position 667, which is often observed in HIV-1 clade C isolates. Based on our results, we propose a somewhat more flexible molecular model of epitope recognition by bnMAb 2F5, which could guide future attempts at designing small-molecule MPER-like vaccines capable of eliciting 2F5-like antibodies.

-	~~{{STRUCTURE_3idm\| PDB=3idm \| SCENE= }}~~	+	Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: vaccine design implications.,Bryson S, Julien JP, Hynes RC, Pai EF J Virol. 2009 Nov;83(22):11862-75. Epub 2009 Sep 9. PMID:19740978<ref>PMID:19740978</ref>

-	~~===Crystal structure~~ of the ~~HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19740978}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3idm]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA].~~	+

	==See Also==		==See Also==
	*[[Monoclonal Antibody\|Monoclonal Antibody]]		*[[Monoclonal Antibody\|Monoclonal Antibody]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019740978<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bryson, S.]]		[[Category: Bryson, S.]]

OCA at 21:04, 20 October 2012

OCA — Sat, 20 Oct 2012 21:04:21 GMT

←Older revision		Revision as of 21:04, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[3idm]] is a 3 chain structure ~~of [[Monoclonal Antibody]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA].	+	[[3idm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA].

	==See Also==		==See Also==

OCA: Protected "3idm" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 12:30:43 GMT

Protected "3idm" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:30, 27 July 2012

OCA at 12:30, 27 July 2012

OCA — Fri, 27 Jul 2012 12:30:41 GMT

←Older revision		Revision as of 12:30, 27 July 2012
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-	~~{{Seed}}~~	+	[[Image:3idm.png\|left\|200px]]
-	[[Image:3idm.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3idm", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3idm\| PDB=3idm \| SCENE= }}		{{STRUCTURE_3idm\| PDB=3idm \| SCENE= }}

	===Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS===		===Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19740978}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19740978 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19740978}}		{{ABSTRACT_PUBMED_19740978}}

	==About this Structure==		==About this Structure==
-	~~3IDM~~ is a 3 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA].	+	[[3idm]] is a 3 chain structure of [[Monoclonal Antibody]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA].
		+
		+	==See Also==
		+	*[[Monoclonal Antibody\|Monoclonal Antibody]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19740978~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019740978</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bryson, S.]]		[[Category: Bryson, S.]]
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	[[Category: Immune system]]		[[Category: Immune system]]
	[[Category: Mper]]		[[Category: Mper]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:40:57 2010''

OCA at 07:40, 3 February 2010

OCA — Wed, 03 Feb 2010 07:40:57 GMT

←Older revision		Revision as of 07:40, 3 February 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3idm.jpg\|left\|200px]]

-	The ~~entry 3idm~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3idm", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3idm\| PDB=3idm \| SCENE= }}

-	~~Authors: Julien, J.~~-~~P., Bryson, S., Pai, E.F.~~	+	===Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS===

-	Description: Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep~~ 9 09:06:~~16 2009~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19740978}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19740978 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19740978}}
		+
		+	==About this Structure==
		+	3IDM is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDM OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19740978</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Bryson, S.]]
		+	[[Category: Julien, J P.]]
		+	[[Category: Pai, E F.]]
		+	[[Category: 2f5]]
		+	[[Category: Gp41]]
		+	[[Category: Hiv-1]]
		+	[[Category: Immune system]]
		+	[[Category: Mper]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:40:57 2010''