5tfw - Revision history

OCA at 12:59, 4 October 2023

2023-10-04T12:59:55Z

←Older revision		Revision as of 12:59, 4 October 2023
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	<StructureSection load='5tfw' size='340' side='right'caption='[[5tfw]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='5tfw' size='340' side='right'caption='[[5tfw]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tfw]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~] and [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TFW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TFW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tfw]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TFW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TFW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1~~,2~~-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.168Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~IGHV3-1505 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~, ~~IGLV3~~-~~1901 ([http:~~/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5tfw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tfw OCA], [~~http~~://pdbe.org/5tfw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tfw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tfw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tfw 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=5tfw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tfw OCA], [https://pdbe.org/5tfw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tfw RCSB], [https://www.ebi.ac.uk/pdbsum/5tfw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tfw ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Irimia, A]]	+	[[Category: Irimia A]]
-	[[Category: Wilson~~, I A]]~~	+	[[Category: Wilson IA]]
-	~~[[Category: 10e8 fab]]~~	+
-	~~[[Category: Hiv-1 gp41 mper]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Lipid membrane~~]]	+

OCA at 16:55, 11 December 2019

2019-12-11T16:55:16Z

←Older revision		Revision as of 16:55, 11 December 2019
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	==Crystal structure of 10E8 Fab light chain mutant2 against the MPER region of the HIV-1 Env, in complex with T117v2 epitope scaffold==		==Crystal structure of 10E8 Fab light chain mutant2 against the MPER region of the HIV-1 Env, in complex with T117v2 epitope scaffold==
-	<StructureSection load='5tfw' size='340' side='right' caption='[[5tfw]], [[Resolution\|resolution]] 2.17Å' scene=''>	+	<StructureSection load='5tfw' size='340' side='right'caption='[[5tfw]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tfw]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TFW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TFW FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tfw]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TFW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TFW FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5tfw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5tfw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Irimia, A]]		[[Category: Irimia, A]]

OCA at 19:06, 15 November 2017

2017-11-15T19:06:55Z

←Older revision		Revision as of 19:06, 15 November 2017
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	<StructureSection load='5tfw' size='340' side='right' caption='[[5tfw]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='5tfw' size='340' side='right' caption='[[5tfw]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tfw]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TFW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TFW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tfw]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TFW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TFW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHV3-1505 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), IGLV3-1901 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5tfw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tfw OCA], [http://pdbe.org/5tfw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tfw RCSB], [http://www.ebi.ac.uk/pdbsum/5tfw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tfw 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=5tfw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tfw OCA], [http://pdbe.org/5tfw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tfw RCSB], [http://www.ebi.ac.uk/pdbsum/5tfw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tfw ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Synthetic construct sequences]]
	[[Category: Irimia, A]]		[[Category: Irimia, A]]
	[[Category: Wilson, I A]]		[[Category: Wilson, I A]]

OCA at 16:49, 9 March 2017

2017-03-09T16:49:28Z

←Older revision		Revision as of 16:49, 9 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tfw is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of 10E8 Fab light chain mutant2 against the MPER region of the HIV-1 Env, in complex with T117v2 epitope scaffold==
		+	<StructureSection load='5tfw' size='340' side='right' caption='[[5tfw]], [[Resolution\|resolution]] 2.17Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5tfw]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TFW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TFW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5tfw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tfw OCA], [http://pdbe.org/5tfw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tfw RCSB], [http://www.ebi.ac.uk/pdbsum/5tfw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tfw ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Among broadly neutralizing antibodies to HIV, 10E8 exhibits greater neutralizing breadth than most. Consequently, this antibody is the focus of prophylactic/therapeutic development. The 10E8 epitope has been identified as the conserved membrane proximal external region (MPER) of gp41 subunit of the envelope (Env) viral glycoprotein and is a major vaccine target. However, the MPER is proximal to the viral membrane and may be laterally inserted into the membrane in the Env prefusion form. Nevertheless, 10E8 has not been reported to have significant lipid-binding reactivity. Here we report x-ray structures of lipid complexes with 10E8 and a scaffolded MPER construct and mutagenesis studies that provide evidence that the 10E8 epitope is composed of both MPER and lipid. 10E8 engages lipids through a specific lipid head group interaction site and a basic and polar surface on the light chain. In the model that we constructed, the MPER would then be essentially perpendicular to the virion membrane during 10E8 neutralization of HIV-1. As the viral membrane likely also plays a role in selecting for the germline antibody as well as size and residue composition of MPER antibody complementarity determining regions, the identification of lipid interaction sites and the MPER orientation with regard to the viral membrane surface during 10E8 engagement can be of great utility for immunogen and therapeutic design.

-	~~Authors~~:	+	Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design.,Irimia A, Serra AM, Sarkar A, Jacak R, Kalyuzhniy O, Sok D, Saye-Francisco KL, Schiffner T, Tingle R, Kubitz M, Adachi Y, Stanfield RL, Deller MC, Burton DR, Schief WR, Wilson IA PLoS Pathog. 2017 Feb 22;13(2):e1006212. doi: 10.1371/journal.ppat.1006212., eCollection 2017 Feb. PMID:28225819<ref>PMID:28225819</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5tfw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Irimia, A]]
		+	[[Category: Wilson, I A]]
		+	[[Category: 10e8 fab]]
		+	[[Category: Hiv-1 gp41 mper]]
		+	[[Category: Immune system]]
		+	[[Category: Lipid membrane]]

OCA at 19:45, 22 December 2016

2016-12-22T19:45:13Z

←Older revision		Revision as of 19:45, 22 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5tfw is ON HOLD	+	The entry 5tfw is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5tfw" [edit=sysop:move=sysop]

2016-10-05T20:01:41Z

Protected "5tfw" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:01, 5 October 2016

OCA: New page: '''Unreleased structure''' The entry 5tfw is ON HOLD Authors: Description: Category: Unreleased Structures

2016-10-05T20:01:40Z

New page: '''Unreleased structure''' The entry 5tfw is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5tfw is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]