3lev - Revision history

OCA at 09:23, 30 October 2024

2024-10-30T09:23:27Z

← Older revision		Revision as of 09:23, 30 October 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/le/3lev_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/le/3lev_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 08:35, 6 September 2023

2023-09-06T08:35:57Z

← Older revision		Revision as of 08:35, 6 September 2023
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	<StructureSection load='3lev' size='340' side='right'caption='[[3lev]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3lev' size='340' side='right'caption='[[3lev]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3lev]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_25104 Atcc 25104~~] and [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LEV FirstGlance]. <br>		<table><tr><td colspan='2'>[[3lev]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LEV FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>~~, ~~<scene name='pdbligand=ATP:ADENOSINE-~~5~~-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.5Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3les\|3les]], [[3lex\|3lex]], [[3ley\|3ley]], [[1tji\|1tji]]~~</~~div~~><~~/td~~></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">SIGMA FACTOR SIGA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])~~</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=3lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lev OCA], [https://pdbe.org/3lev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lev RCSB], [https://www.ebi.ac.uk/pdbsum/3lev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lev 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=3lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lev OCA], [https://pdbe.org/3lev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lev RCSB], [https://www.ebi.ac.uk/pdbsum/3lev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lev ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/~~Q9EZJ8_THEAQ Q9EZJ8_THEAQ]~~] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released ~~(By similarity)~~.[~~RuleBase~~:~~RU000715~~]		[https://www.uniprot.org/uniprot/SIGA_THEAQ SIGA_THEAQ] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.[HAMAP-Rule:MF_00963]<ref>PMID:11114902</ref> <ref>PMID:11931761</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Atcc 25104]]~~		[[Category: Homo sapiens]]
	~~[[Category: Human~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Baker, D]]		[[Category: Thermus aquaticus]]
	[[Category: Guenaga~~, F J~~]]		[[Category: Baker D]]
	[[Category: Kwong~~, P D~~]]		[[Category: Guenaga FJ]]
	[[Category: Ofek, G]]		[[Category: Kwong PD]]
	[[Category: Schief~~, W R~~]]		[[Category: Ofek G]]
	[[Category: Skinner, J]]		[[Category: Schief WR]]
	[[Category: Wyatt, R]]		[[Category: Skinner J]]
	~~[[Category: Epitope]]~~		[[Category: Wyatt R]]
	~~[[Category: Gp41]]~~
	~~[[Category: Graft]]~~
	~~[[Category: Hiv-1]]~~
	~~[[Category: Immune system]]~~
	~~[[Category: Monoclonal antibody]]~~
	~~[[Category: Re-elicitation]]~~
	~~[[Category: Scaffold]]~~
	~~[[Category: Sigma factor]]~~
	~~[[Category: Transplant]]~~
	~~[[Category: Vaccine design~~]]

OCA at 10:36, 31 March 2021

2021-03-31T10:36:58Z

← Older revision		Revision as of 10:36, 31 March 2021
Line 1:		Line 1:

	==HIV-1 antibody 2F5 in complex with epitope scaffold ES2==		==HIV-1 antibody 2F5 in complex with epitope scaffold ES2==
	<StructureSection load='3lev' size='340' side='right' caption='[[3lev]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3lev' size='340' side='right'caption='[[3lev]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3lev]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104] and [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3LEV FirstGlance]. <br>		<table><tr><td colspan='2'>[[3lev]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104] and [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LEV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3les\|3les]], [[3lex\|3lex]], [[3ley\|3ley]], [[1tji\|1tji]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3les\|3les]], [[3lex\|3lex]], [[3ley\|3ley]], [[1tji\|1tji]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIGMA FACTOR SIGA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIGMA FACTOR SIGA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=3lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lev OCA], [~~http~~://pdbe.org/3lev PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3lev RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3lev PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3lev 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=3lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lev OCA], [https://pdbe.org/3lev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lev RCSB], [https://www.ebi.ac.uk/pdbsum/3lev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lev ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/Q9EZJ8_THEAQ Q9EZJ8_THEAQ]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715]		[[https://www.uniprot.org/uniprot/Q9EZJ8_THEAQ Q9EZJ8_THEAQ]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[Sigma factor\|Sigma factor]]		*[[Sigma factor 3D structures\|Sigma factor 3D structures]]
			*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 41:
	[[Category: Atcc 25104]]		[[Category: Atcc 25104]]
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
	[[Category: Guenaga, F J]]		[[Category: Guenaga, F J]]

OCA at 06:53, 2 January 2019

2019-01-02T06:53:00Z

← Older revision		Revision as of 06:53, 2 January 2019
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/le/3lev_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/le/3lev_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 32:		Line 32:

	==See Also==		==See Also==
			*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[Sigma factor\|Sigma factor]]		*[[Sigma factor\|Sigma factor]]
	*[[3D structures of antibody\|3D structures of antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:27, 4 August 2016

2016-08-04T19:27:25Z

← Older revision		Revision as of 19:27, 4 August 2016
Line 1:		Line 1:

	==HIV-1 antibody 2F5 in complex with epitope scaffold ES2==		==HIV-1 antibody 2F5 in complex with epitope scaffold ES2==
	<StructureSection load='3lev' size='340' side='right' caption='[[3lev]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3lev' size='340' side='right' caption='[[3lev]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~] and [http://en.wikipedia.org/wiki/~~Thermus_aquaticus Thermus aquaticus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LEV FirstGlance]. <br>		<table><tr><td colspan='2'>[[3lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LEV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3les\|3les]], [[3lex\|3lex]], [[3ley\|3ley]], [[1tji\|1tji]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3les\|3les]], [[3lex\|3lex]], [[3ley\|3ley]], [[1tji\|1tji]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIGMA FACTOR SIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ~~Thermus aquaticus~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIGMA FACTOR SIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=3lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lev RCSB], [http://www.ebi.ac.uk/pdbsum/3lev 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=3lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lev OCA], [http://pdbe.org/3lev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lev RCSB], [http://www.ebi.ac.uk/pdbsum/3lev PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lev ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=3lev ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3lev" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Antibody\|Antibody]]
	*[[Sigma factor\|Sigma factor]]		*[[Sigma factor\|Sigma factor]]
			*[[3D structures of antibody\|3D structures of antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Atcc 25104]]
	[[Category: ~~Thermus aquaticus~~]]		[[Category: Human]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
	[[Category: Guenaga, F J]]		[[Category: Guenaga, F J]]

OCA at 12:24, 25 December 2014

2014-12-25T12:24:03Z

← Older revision		Revision as of 12:24, 25 December 2014
Line 8:		Line 8:
	<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=3lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lev RCSB], [http://www.ebi.ac.uk/pdbsum/3lev 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=3lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lev RCSB], [http://www.ebi.ac.uk/pdbsum/3lev PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/Q9EZJ8_THEAQ Q9EZJ8_THEAQ]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:55, 18 December 2014

2014-12-18T16:55:26Z

← Older revision		Revision as of 16:55, 18 December 2014
Line 1:		Line 1:
	~~{{STRUCTURE_3lev~~\| ~~PDB~~=3lev \| ~~SCENE~~= }}		==HIV-1 antibody 2F5 in complex with epitope scaffold ES2==
	===HIV-1 antibody 2F5 in complex with epitope ~~scaffold ES2===~~		<StructureSection load='3lev' size='340' side='right' caption='[[3lev]], [[Resolution\|resolution]] 2.50Å' scene=''>
	~~{{ABSTRACT_PUBMED_20876137}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[3lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LEV FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3les\|3les]], [[3lex\|3lex]], [[3ley\|3ley]], [[1tji\|1tji]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIGMA FACTOR SIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</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=3lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lev RCSB], [http://www.ebi.ac.uk/pdbsum/3lev 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/le/3lev_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 ==
			Elicitation of antibodies against targets that are immunorecessive, cryptic, or transient in their native context has been a challenge for vaccine design. Here we demonstrate the elicitation of structure-specific antibodies against the HIV-1 gp41 epitope of the broadly neutralizing antibody 2F5. This conformationally flexible region of gp41 assumes mostly helical conformations but adopts a kinked, extended structure when bound by antibody 2F5. Computational techniques were employed to transplant the 2F5 epitope into select acceptor scaffolds. The resultant "2F5-epitope scaffolds" possessed nanomolar affinity for antibody 2F5 and a range of epitope flexibilities and antigenic specificities. Crystallographic characterization of the epitope scaffold with highest affinity and antigenic discrimination confirmed good to near perfect attainment of the target conformation for the gp41 molecular graft in free and 2F5-bound states, respectively. Animals immunized with 2F5-epitope scaffolds showed levels of graft-specific immune responses that correlated with graft flexibility (p < 0.04), while antibody responses against the graft-as dissected residue-by-residue with alanine substitutions-resembled more closely those of 2F5 than sera elicited with flexible or cyclized peptides, a resemblance heightened by heterologous prime-boost. Lastly, crystal structures of a gp41 peptide in complex with monoclonal antibodies elicited by the 2F5-epitope scaffolds revealed that the elicited antibodies induce gp41 to assume its 2F5-recognized shape. Epitope scaffolds thus provide a means to elicit antibodies that recognize a predetermined target shape and sequence, even if that shape is transient in nature, and a means by which to dissect factors influencing such elicitation.

	~~==Function==~~		Elicitation of structure-specific antibodies by epitope scaffolds.,Ofek G, Guenaga FJ, Schief WR, Skinner J, Baker D, Wyatt R, Kwong PD Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):17880-7. Epub 2010 Sep 27. PMID:20876137<ref>PMID:20876137</ref>
	~~[[http://www~~.~~uniprot~~.~~org/uniprot/Q9EZJ8_THEAQ Q9EZJ8_THEAQ]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released~~ (~~By similarity~~).~~[RuleBase~~:~~RU000715]~~

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[3lev]] is~~ a ~~3 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens] and [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=3LEV OCA].~~		</div>

	==See Also==		==See Also==
	*[[Antibody\|Antibody]]		*[[Antibody\|Antibody]]
			*[[Sigma factor\|Sigma factor]]
	==~~Reference~~==		== References ==
	~~<ref group="xtra">PMID:020876137</ref>~~<references ~~group="xtra"~~/><~~references~~/>		<references/>
			__TOC__
			</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
	[[Category: Baker, D.]]		[[Category: Baker, D]]
	[[Category: Guenaga, F J.]]		[[Category: Guenaga, F J]]
	[[Category: Kwong, P D.]]		[[Category: Kwong, P D]]
	[[Category: Ofek, G.]]		[[Category: Ofek, G]]
	[[Category: Schief, W R.]]		[[Category: Schief, W R]]
	[[Category: Skinner, J.]]		[[Category: Skinner, J]]
	[[Category: Wyatt, R~~.]]~~		[[Category: Wyatt, R]]
	~~[[Category: 2f5~~]]
	[[Category: Epitope]]		[[Category: Epitope]]
	[[Category: Gp41]]		[[Category: Gp41]]

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

2013-04-04T20:44:12Z

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

← Older revision	Revision as of 20:44, 4 April 2013
(No difference)

OCA at 20:44, 4 April 2013

2013-04-04T20:44:05Z

← Older revision		Revision as of 20:44, 4 April 2013
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	~~{{Seed}}~~
	~~[[Image:3lev.png\|left\|200px]]~~

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3lev", 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_3lev\| PDB=3lev \| SCENE= }}		{{STRUCTURE_3lev\| PDB=3lev \| SCENE= }}

	===HIV-1 antibody 2F5 in complex with epitope scaffold ES2===		===HIV-1 antibody 2F5 in complex with epitope scaffold ES2===
			{{ABSTRACT_PUBMED_20876137}}

			==Function==
			[[http://www.uniprot.org/uniprot/Q9EZJ8_THEAQ Q9EZJ8_THEAQ]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715]

	~~<!--~~		==About this Structure==
	~~The line below~~ this ~~paragraph, {{ABSTRACT_PUBMED_20876137}}, adds the Publication Abstract to the page~~		[[3lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEV OCA].
	~~(as it appears on PubMed at~~ http://~~www~~.~~pubmed~~.~~gov), where 20876137~~ is ~~the PubMed ID number~~.
	-->
	~~{{ABSTRACT_PUBMED_20876137}}~~

	==~~About this Structure~~==		==See Also==
	~~3LEV is a 3 chains structure with sequences from~~ [~~http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and~~ [~~http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus~~]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEV OCA~~].		*[[Antibody\|Antibody]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~20876137~~</ref><references group="xtra"/>		<ref group="xtra">PMID:020876137</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
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	[[Category: Transplant]]		[[Category: Transplant]]
	[[Category: Vaccine design]]		[[Category: Vaccine design]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 24 13:37:57 2010''~~

OCA at 10:26, 24 November 2010

2010-11-24T10:26:44Z

← Older revision		Revision as of 10:26, 24 November 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
	[[Image:3lev.~~jpg~~\|left\|200px]]		[[Image:3lev.png\|left\|200px]]

	<!--		<!--
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	===HIV-1 antibody 2F5 in complex with epitope scaffold ES2===		===HIV-1 antibody 2F5 in complex with epitope scaffold ES2===


			<!--
			The line below this paragraph, {{ABSTRACT_PUBMED_20876137}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 20876137 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_20876137}}

	==About this Structure==		==About this Structure==
	3LEV is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEV OCA].		3LEV is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEV OCA].

			==Reference==
			<ref group="xtra">PMID:20876137</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
Line 37:		Line 46:
	[[Category: Vaccine design]]		[[Category: Vaccine design]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep 29 08~~:14:24 2010''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 24 13:37:57 2010''