4xml - Revision history

OCA at 17:43, 26 April 2023

2023-04-26T17:43:03Z

←Older revision		Revision as of 17:43, 26 April 2023
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	<StructureSection load='4xml' size='340' side='right'caption='[[4xml]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='4xml' size='340' side='right'caption='[[4xml]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xml]] is a 2 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=4XML OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XML FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xml]] is a 2 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=4XML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XML FirstGlance]. <br>
-	</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=4xml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xml OCA], [~~http~~://pdbe.org/4xml PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xml RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xml PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xml ProSAT]</span></td></tr>	+	</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=4xml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xml OCA], [https://pdbe.org/4xml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xml RCSB], [https://www.ebi.ac.uk/pdbsum/4xml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xml 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: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kong, X P]]	+	[[Category: Kong X-P]]
-	[[Category: Pan, R]]	+	[[Category: Pan R]]
-	~~[[Category: Hiv-1 gp120]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Monoclonal antibody~~]]	+

OCA at 15:49, 11 December 2019

2019-12-11T15:49:22Z

←Older revision		Revision as of 15:49, 11 December 2019
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	==Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424==		==Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424==
-	<StructureSection load='4xml' size='340' side='right' caption='[[4xml]], [[Resolution\|resolution]] 2.68Å' scene=''>	+	<StructureSection load='4xml' size='340' side='right'caption='[[4xml]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xml]] is a 2 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=4XML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XML FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xml]] is a 2 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=4XML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XML FirstGlance]. <br>
Line 17:		Line 17:

	==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 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Kong, X P]]		[[Category: Kong, X P]]
	[[Category: Pan, R]]		[[Category: Pan, R]]

OCA at 15:32, 15 November 2017

2017-11-15T15:32:29Z

←Older revision		Revision as of 15:32, 15 November 2017
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	<StructureSection load='4xml' size='340' side='right' caption='[[4xml]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='4xml' size='340' side='right' caption='[[4xml]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xml]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XML FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xml]] is a 2 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=4XML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XML FirstGlance]. <br>
	</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=4xml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xml OCA], [http://pdbe.org/4xml PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xml RCSB], [http://www.ebi.ac.uk/pdbsum/4xml PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xml ProSAT]</span></td></tr>		</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=4xml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xml OCA], [http://pdbe.org/4xml PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xml RCSB], [http://www.ebi.ac.uk/pdbsum/4xml PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xml ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Kong, X P]]		[[Category: Kong, X P]]
	[[Category: Pan, R]]		[[Category: Pan, R]]

OCA at 16:09, 17 May 2017

2017-05-17T16:09:51Z

←Older revision		Revision as of 16:09, 17 May 2017
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		+
	==Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424==		==Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424==
	<StructureSection load='4xml' size='340' side='right' caption='[[4xml]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='4xml' size='340' side='right' caption='[[4xml]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xml]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XML FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xml]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XML FirstGlance]. <br>
-	</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=4xml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xml OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xml RCSB], [http://www.ebi.ac.uk/pdbsum/4xml PDBsum]</span></td></tr>	+	</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=4xml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xml OCA], [http://pdbe.org/4xml PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xml RCSB], [http://www.ebi.ac.uk/pdbsum/4xml PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xml ProSAT]</span></td></tr>
	</table>		</table>
	<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 4xml" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[3D structures of monoclonal antibody\|3D structures of monoclonal antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:46, 12 August 2015

2015-08-12T08:46:43Z

←Older revision		Revision as of 08:46, 12 August 2015
Line 20:		Line 20:
	[[Category: Pan, R]]		[[Category: Pan, R]]
	[[Category: Hiv-1 gp120]]		[[Category: Hiv-1 gp120]]
		+	[[Category: Immune system]]
	[[Category: Monoclonal antibody]]		[[Category: Monoclonal antibody]]

OCA at 14:46, 8 July 2015

2015-07-08T14:46:51Z

←Older revision		Revision as of 14:46, 8 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424==
		+	<StructureSection load='4xml' size='340' side='right' caption='[[4xml]], [[Resolution\|resolution]] 2.68Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xml]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XML FirstGlance]. <br>
		+	</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=4xml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xml OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xml RCSB], [http://www.ebi.ac.uk/pdbsum/4xml PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The V3 region of HIV-1 gp120 is important for virus-coreceptor interaction and highly immunogenic. Although most anti-V3 antibodies neutralize only the sensitive Tier 1 viruses, anti-V3 antibodies effective against the more resistant viruses exist, and a better understanding about these antibodies and their epitopes would be beneficial for the development of novel vaccine immunogens against HIV. The HIV-1 isolate JRFL with its cryptic V3 is resistant to most V3-specific monoclonal antibodies (mAbs). However, the V3 mAb 2424 achieves 100% neutralization against JRFL. 2424 is encoded by IgH V3-53 and IgL V2-28 genes, a pairing rarely used by the other V3 mAbs.. 2424 also has distinct binding and neutralization profiles. Studies of 2424-mediated neutralization of JRFL produced with a mannosidase inhibitor further revealed that its neutralizing activity is unaffected by the glycan composition of the virus envelope. To understand the distinct activity of 2424, we determined the crystal structure of 2424 Fab in complex with a JRFL V3 peptide, and showed that the 2424 epitope is located at the tip of the V3 crown (307IHIGPGRAFY318), dominated by interactions with HisP308, ProP313, and ArgP315. The binding mode of 2424 is similar to that of the well-characterized 447-52D, although 2424 is more side-chain dependent. The 2424 epitope is focused on the very apex of V3, away from nearby glycans, facilitating antibody access. This feature distinguishes the 2424 epitope from the other V3 crown epitopes and indicates that the tip of V3 is a potential site to target and incorporate into HIV vaccine immunogens. IMPORTANCE: HIV/AIDS vaccines are crucial for controlling the HIV epidemics that continue to afflict millions of people worldwide. However, HIV vaccine development has been hampered by significant scientific challenges, one of which is the inability of HIV vaccine candidates evaluated thus far to elicit production of potent and broadly neutralizing antibodies. The V3 loop is one of the few immunogenic targets on the virus envelope glycoprotein that can induce neutralizing antibodies, but in many viruses, parts of V3 are inaccessible for antibody recognition. This study examined a V3-specific monoclonal antibody that can completely neutralize HIV-1 JRFL, a virus isolate resistant to most V3 antibodies. Our data reveal that this antibody recognizes the most distal tip of V3 that is not as occluded as other parts of V3. Hence, the epitope of 2424 is in one of the vulnerable sites on the virus that may be exploited in designing HIV vaccine immunogens.

-	~~The entry 4xml is ON HOLD until Paper Publication~~	+	Functional and structural characterization of human V3-specific monoclonal antibody 2424 with neutralizing activity against HIV-1 JRFL.,Kumar R, Pan R, Upadhyay C, Mayr L, Cohen S, Wang XH, Balasubramanian P, Nadas A, Seaman MS, Zolla-Pazner S, Gorny MK, Kong XP, Hioe CE J Virol. 2015 Jun 24. pii: JVI.01280-15. PMID:26109728<ref>PMID:26109728</ref>

-	~~Authors: Pan~~, R.~~, Kong, X~~.-P.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kong, X P]]
	[[Category: Pan, R]]		[[Category: Pan, R]]
-	[[Category: ~~Kong, X.~~-P]]	+	[[Category: Hiv-1 gp120]]
		+	[[Category: Monoclonal antibody]]

OCA at 09:50, 11 March 2015

2015-03-11T09:50:40Z

←Older revision		Revision as of 09:50, 11 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Pan, R., Kong, X.-P.		Authors: Pan, R., Kong, X.-P.

OCA at 11:28, 18 February 2015

2015-02-18T11:28:56Z

←Older revision		Revision as of 11:28, 18 February 2015
Line 3:		Line 3:
	The entry 4xml is ON HOLD		The entry 4xml is ON HOLD

-	Authors: ~~Ruimin~~ Pan, ~~Xiang-Peng~~ Kong	+	Authors: Pan, R., Kong, X.-P.

	Description: Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424		Description: Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Ruimin~~ Pan, ~~Xiang-Peng~~ Kong]]	+	[[Category: Pan, R]]
		+	[[Category: Kong, X.-P]]

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

2015-01-21T16:01:51Z

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

←Older revision

Revision as of 16:01, 21 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xml is ON HOLD Authors: Ruimin Pan, Xiang-Peng Kong Description: Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 242...

2015-01-21T16:01:50Z

New page: '''Unreleased structure''' The entry 4xml is ON HOLD Authors: Ruimin Pan, Xiang-Peng Kong Description: Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 242...

New page

'''Unreleased structure'''

The entry 4xml is ON HOLD

Authors: Ruimin Pan, Xiang-Peng Kong

Description: Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424
[[Category: Unreleased Structures]]
[[Category: Ruimin Pan, Xiang-Peng Kong]]