4xbg - Revision history

OCA at 07:43, 27 September 2023

2023-09-27T07:43:26Z

←Older revision		Revision as of 07:43, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xbg]] is a 12 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=4XBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XBG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xbg]] is a 12 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=4XBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XBG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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]] 2.73Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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=4xbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xbg OCA], [https://pdbe.org/4xbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xbg RCSB], [https://www.ebi.ac.uk/pdbsum/4xbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xbg 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=4xbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xbg OCA], [https://pdbe.org/4xbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xbg RCSB], [https://www.ebi.ac.uk/pdbsum/4xbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xbg ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:21, 12 April 2023

2023-04-12T21:21:15Z

←Older revision		Revision as of 21:21, 12 April 2023
Line 3:		Line 3:
	<StructureSection load='4xbg' size='340' side='right'caption='[[4xbg]], [[Resolution\|resolution]] 2.73Å' scene=''>		<StructureSection load='4xbg' size='340' side='right'caption='[[4xbg]], [[Resolution\|resolution]] 2.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xbg]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XBG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XBG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xbg]] is a 12 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=4XBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XBG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xaw\|4xaw]], [[4xbe\|4xbe]], [[4xc1\|4xc1]], [[4xc3\|4xc3]], [[4xbp\|4xbp]], [[4xce\|4xce]], [[4xcc\|4xcc]], [[4xcf\|4xcf]], [[4xcn\|4xcn]], [[4xcy\|4xcy]]</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=4xbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xbg OCA], [https://pdbe.org/4xbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xbg RCSB], [https://www.ebi.ac.uk/pdbsum/4xbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xbg 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=4xbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xbg OCA], [~~http~~://pdbe.org/4xbg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xbg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xbg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xbg ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Irimia, A]]	+	[[Category: Irimia A]]
-	[[Category: Stanfield~~, R L~~]]	+	[[Category: Stanfield RL]]
-	[[Category: Wilson~~, I A]]~~	+	[[Category: Wilson IA]]
-	~~[[Category: Human anti gp41 hiv-1 4e10 fab]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Membrane lipid]]~~	+
-	~~[[Category: Phosphatidic acid~~]]	+

OCA at 07:32, 29 May 2019

2019-05-29T07:32:36Z

←Older revision		Revision as of 07:32, 29 May 2019
Line 1:		Line 1:
		+
	==Crystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 PA): 2.73 A resolution==		==Crystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 PA): 2.73 A resolution==
-	<StructureSection load='4xbg' size='340' side='right' caption='[[4xbg]], [[Resolution\|resolution]] 2.73Å' scene=''>	+	<StructureSection load='4xbg' size='340' side='right'caption='[[4xbg]], [[Resolution\|resolution]] 2.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xbg]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XBG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XBG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xbg]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XBG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XBG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xaw\|4xaw]], [[4xbe\|4xbe]], [[4xc1\|4xc1]], [[4xc3\|4xc3]], [[4xbp\|4xbp]], [[4xce\|4xce]], [[4xcc\|4xcc]], [[4xcf\|4xcf]], [[4xcn\|4xcn]], [[4xcy\|4xcy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xaw\|4xaw]], [[4xbe\|4xbe]], [[4xc1\|4xc1]], [[4xc3\|4xc3]], [[4xbp\|4xbp]], [[4xce\|4xce]], [[4xcc\|4xcc]], [[4xcf\|4xcf]], [[4xcn\|4xcn]], [[4xcy\|4xcy]]</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=4xbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xbg OCA], [http://pdbe.org/4xbg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xbg RCSB], [http://www.ebi.ac.uk/pdbsum/4xbg 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=4xbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xbg OCA], [http://pdbe.org/4xbg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xbg RCSB], [http://www.ebi.ac.uk/pdbsum/4xbg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xbg ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Irimia, A]]		[[Category: Irimia, A]]
	[[Category: Stanfield, R L]]		[[Category: Stanfield, R L]]

OCA at 15:33, 3 February 2016

2016-02-03T15:33:25Z

←Older revision		Revision as of 15:33, 3 February 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 PA): 2.73 A resolution==
		+	<StructureSection load='4xbg' size='340' side='right' caption='[[4xbg]], [[Resolution\|resolution]] 2.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xbg]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XBG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XBG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xaw\|4xaw]], [[4xbe\|4xbe]], [[4xc1\|4xc1]], [[4xc3\|4xc3]], [[4xbp\|4xbp]], [[4xce\|4xce]], [[4xcc\|4xcc]], [[4xcf\|4xcf]], [[4xcn\|4xcn]], [[4xcy\|4xcy]]</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=4xbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xbg OCA], [http://pdbe.org/4xbg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xbg RCSB], [http://www.ebi.ac.uk/pdbsum/4xbg PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Numerous studies of the anti-HIV-1 envelope glycoprotein 41 (gp41) broadly neutralizing antibody 4E10 suggest that 4E10 also interacts with membrane lipids, but the antibody regions contacting lipids and its orientation with respect to the viral membrane are unknown. Vaccine immunogens capable of re-eliciting these membrane proximal external region (MPER)-like antibodies may require a lipid component to be successful. We performed a systematic crystallographic study of lipid binding to 4E10 to identify lipids bound by the antibody and the lipid-interacting regions. We identified phosphatidic acid, phosphatidylglycerol, and glycerol phosphate as specific ligands for 4E10 in the crystal structures. 4E10 used its CDRH1 loop to bind the lipid head groups, while its CDRH3 interacted with the hydrophobic lipid tails. Identification of the lipid binding sites on 4E10 may aid design of immunogens for vaccines that include a lipid component in addition to the MPER on gp41 for generation of broadly neutralizing antibodies.

-	~~The entry 4xbg is ON HOLD until Mar 16 2017~~	+	Crystallographic Identification of Lipid as an Integral Component of the Epitope of HIV Broadly Neutralizing Antibody 4E10.,Irimia A, Sarkar A, Stanfield RL, Wilson IA Immunity. 2016 Jan 19;44(1):21-31. doi: 10.1016/j.immuni.2015.12.001. Epub 2016, Jan 5. PMID:26777395<ref>PMID:26777395</ref>

-	~~Authors: Irimia~~, A.~~, Stanfield, R~~.~~L., Wilson, I.A~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	<div class="pdbe-citations 4xbg" style="background-color:#fffaf0;"></div>
-	~~[[Category: Unreleased Structures]]~~	+	== References ==
-	~~[[Category: Stanfield, R.L]]~~	+	<references/>
-	~~[[Category: Wilson, I.A]]~~	+	__TOC__
		+	</StructureSection>
	[[Category: Irimia, A]]		[[Category: Irimia, A]]
		+	[[Category: Stanfield, R L]]
		+	[[Category: Wilson, I A]]
		+	[[Category: Human anti gp41 hiv-1 4e10 fab]]
		+	[[Category: Immune system]]
		+	[[Category: Membrane lipid]]
		+	[[Category: Phosphatidic acid]]

OCA at 08:29, 16 December 2015

2015-12-16T08:29:45Z

←Older revision		Revision as of 08:29, 16 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xbg is ON HOLD until ~~Paper Publication~~	+	The entry 4xbg is ON HOLD until Mar 16 2017

	Authors: Irimia, A., Stanfield, R.L., Wilson, I.A.		Authors: Irimia, A., Stanfield, R.L., Wilson, I.A.

OCA at 23:07, 30 November 2015

2015-11-30T23:07:10Z

←Older revision		Revision as of 23:07, 30 November 2015
Line 7:		Line 7:
	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Irimia, A]]
	[[Category: Stanfield, R.L]]		[[Category: Stanfield, R.L]]
	[[Category: Wilson, I.A]]		[[Category: Wilson, I.A]]
		+	[[Category: Irimia, A]]

OCA at 10:11, 22 July 2015

2015-07-22T10:11:25Z

←Older revision		Revision as of 10:11, 22 July 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xbg is ON HOLD	+	The entry 4xbg is ON HOLD until Paper Publication

	Authors: Irimia, A., Stanfield, R.L., Wilson, I.A.		Authors: Irimia, A., Stanfield, R.L., Wilson, I.A.

OCA at 12:32, 14 January 2015

2015-01-14T12:32:44Z

←Older revision		Revision as of 12:32, 14 January 2015
Line 3:		Line 3:
	The entry 4xbg is ON HOLD		The entry 4xbg is ON HOLD

-	Authors: ~~IRIMIA~~, A., ~~STANFIELD~~, R.L., ~~WILSON~~, I.A.	+	Authors: Irimia, A., Stanfield, R.L., Wilson, I.A.

	Description:		Description:

OCA at 20:48, 24 December 2014

2014-12-24T20:48:57Z

←Older revision		Revision as of 20:48, 24 December 2014
Line 5:		Line 5:
	Authors: IRIMIA, A., STANFIELD, R.L., WILSON, I.A.		Authors: IRIMIA, A., STANFIELD, R.L., WILSON, I.A.

-	Description:	+	Description:
		+	[[Category: Unreleased Structures]]
		+	[[Category: Irimia, A]]
		+	[[Category: Stanfield, R.L]]
		+	[[Category: Wilson, I.A]]

OCA: Protected "4xbg" [edit=sysop:move=sysop]

2014-12-24T10:05:09Z

Protected "4xbg" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:05, 24 December 2014