4q2z - Revision history

OCA at 17:26, 20 September 2023

2023-09-20T17:26:45Z

←Older revision		Revision as of 17:26, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4q2z]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Macaca_mulatta Macaca mulatta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q2Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q2Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[4q2z]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Macaca_mulatta Macaca mulatta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q2Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q2Z FirstGlance]. <br>
-	</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=4q2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q2z OCA], [https://pdbe.org/4q2z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q2z RCSB], [https://www.ebi.ac.uk/pdbsum/4q2z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q2z ProSAT]</span></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]] 1.93Å</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=4q2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q2z OCA], [https://pdbe.org/4q2z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q2z RCSB], [https://www.ebi.ac.uk/pdbsum/4q2z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q2z ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:41, 8 February 2023

2023-02-08T07:41:37Z

←Older revision		Revision as of 07:41, 8 February 2023
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	<StructureSection load='4q2z' size='340' side='right'caption='[[4q2z]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='4q2z' size='340' side='right'caption='[[4q2z]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4q2z]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Macmu Macmu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q2Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Q2Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4q2z]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Macaca_mulatta Macaca mulatta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q2Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q2Z FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ktd\|4ktd]], [[4kte\|4kte]]</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=4q2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q2z OCA], [https://pdbe.org/4q2z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q2z RCSB], [https://www.ebi.ac.uk/pdbsum/4q2z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q2z 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=4q2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q2z OCA], [~~http~~://pdbe.org/4q2z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4q2z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4q2z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4q2z 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]]
		+	*[[Sandbox 20009\|Sandbox 20009]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Macmu~~]]	+	[[Category: Macaca mulatta]]
-	[[Category: Bale, S]]	+	[[Category: Bale S]]
-	[[Category: Guenaga, J]]	+	[[Category: Guenaga J]]
-	[[Category: Hedestam~~, G B.K~~]]	+	[[Category: Hedestam GBK]]
-	[[Category: Li, Y]]	+	[[Category: Li Y]]
-	[[Category: Mascola, J]]	+	[[Category: Mascola J]]
-	[[Category: McKee, K]]	+	[[Category: McKee K]]
-	[[Category: Navis, M]]	+	[[Category: Navis M]]
-	[[Category: Phad, G]]	+	[[Category: Phad G]]
-	[[Category: Soldemo, M]]	+	[[Category: Soldemo M]]
-	[[Category: Sundling, C]]	+	[[Category: Sundling C]]
-	[[Category: Tran, K]]	+	[[Category: Tran K]]
-	[[Category: Wilson, R]]	+	[[Category: Wilson R]]
-	[[Category: Wyatt~~, R T]]~~	+	[[Category: Wyatt RT]]
-	~~[[Category: Fab fragment]]~~	+
-	~~[[Category: Hiv viral envelope glycoprotein neutralization]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 09:06, 24 April 2019

2019-04-24T09:06:39Z

←Older revision		Revision as of 09:06, 24 April 2019
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	==Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate==		==Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate==
-	<StructureSection load='4q2z' size='340' side='right' caption='[[4q2z]], [[Resolution\|resolution]] 1.93Å' scene=''>	+	<StructureSection load='4q2z' size='340' side='right'caption='[[4q2z]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4q2z]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q2Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q2Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4q2z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Macmu Macmu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q2Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q2Z FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ktd\|4ktd]], [[4kte\|4kte]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ktd\|4ktd]], [[4kte\|4kte]]</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=4q2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q2z OCA], [http://pdbe.org/4q2z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q2z RCSB], [http://www.ebi.ac.uk/pdbsum/4q2z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q2z 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=4q2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q2z OCA], [http://pdbe.org/4q2z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q2z RCSB], [http://www.ebi.ac.uk/pdbsum/4q2z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q2z ProSAT]</span></td></tr>
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 4q2z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4q2z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Macmu]]
	[[Category: Bale, S]]		[[Category: Bale, S]]
	[[Category: Guenaga, J]]		[[Category: Guenaga, J]]

OCA at 17:15, 4 January 2017

2017-01-04T17:15:52Z

←Older revision		Revision as of 17:15, 4 January 2017
Line 1:		Line 1:
		+
	==Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate==		==Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate==
	<StructureSection load='4q2z' size='340' side='right' caption='[[4q2z]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='4q2z' size='340' side='right' caption='[[4q2z]], [[Resolution\|resolution]] 1.93Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4q2z]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q2Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q2Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[4q2z]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q2Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q2Z FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ktd\|4ktd]], [[4kte\|4kte]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ktd\|4ktd]], [[4kte\|4kte]]</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=4q2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q2z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q2z RCSB], [http://www.ebi.ac.uk/pdbsum/4q2z 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=4q2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q2z OCA], [http://pdbe.org/4q2z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q2z RCSB], [http://www.ebi.ac.uk/pdbsum/4q2z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q2z ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 4q2z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:48, 5 January 2015

2015-01-05T08:48:30Z

←Older revision		Revision as of 08:48, 5 January 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate==
		+	<StructureSection load='4q2z' size='340' side='right' caption='[[4q2z]], [[Resolution\|resolution]] 1.93Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4q2z]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q2Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q2Z FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ktd\|4ktd]], [[4kte\|4kte]]</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=4q2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q2z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q2z RCSB], [http://www.ebi.ac.uk/pdbsum/4q2z PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Broadly neutralizing antibodies (bNAbs) isolated from chronically HIV-1 infected individuals reveal important information regarding how antibodies target conserved determinants of the envelope glycoprotein (Env) spike such as the primary receptor CD4 binding site (CD4bs). Many CD4bs-directed bNAbs use the same heavy (H) chain variable (V) gene segment, VH1-202, suggesting that activation of B cells expressing this allele is linked to the generation of this type of Ab. Here, we identify the rhesus macaque VH1.23 gene segment to be the closest macaque orthologue to the human VH1-2 gene segment, with 92% homology to VH1-202. Of the three amino acids in the VH1-2*02 gene segment that define a motif for VRC01-like antibodies (W50, N58, flanking the HCDR2 region, and R71), the two identified macaque VH1.23 alleles described here encode two. We demonstrate that immunization with soluble Env trimers induced CD4bs-specific VH1.23-using Abs with restricted neutralization breadth. Through alanine scanning and structural studies of one such monoclonal Ab (MAb), GE356, we demonstrate that all three HCDRs are involved in neutralization. This contrasts to the highly potent CD4bs-directed VRC01 class of bNAb, which bind Env predominantly through the HCDR2. Also unlike VRC01, GE356 was minimally modified by somatic hypermutation, its light (L) chain CDRs were of average lengths and it displayed a binding footprint proximal to the trimer axis. These results illustrate that the Env trimer immunogen used here activates B cells encoding a VH1-2 gene segment orthologue, but that the resulting Abs interact distinctly differently with the HIV-1 Env spike compared to VRC01.

-	~~The entry 4q2z is ON HOLD until Paper Publication~~	+	HIV-1 receptor binding site-directed antibodies using a VH1-2 gene segment orthologue are activated by Env trimer immunization.,Navis M, Tran K, Bale S, Phad GE, Guenaga J, Wilson R, Soldemo M, McKee K, Sundling C, Mascola J, Li Y, Wyatt RT, Karlsson Hedestam GB PLoS Pathog. 2014 Aug 28;10(8):e1004337. doi: 10.1371/journal.ppat.1004337., eCollection 2014 Aug. PMID:25166308<ref>PMID:25166308</ref>

-	~~Authors: Navis~~, M.~~, Tran, K~~., Bale, S., ~~Phad~~, G., ~~Guenaga~~, J., ~~Wilson~~, R., Soldemo, M~~., McKee, K.,~~ Sundling, C., ~~Mascola, J., Li, Y.~~, Wyatt, R.T~~., Hedestam, G.B.K.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: Fab fragment ~~of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bale, S]]
		+	[[Category: Guenaga, J]]
		+	[[Category: Hedestam, G B.K]]
		+	[[Category: Li, Y]]
		+	[[Category: Mascola, J]]
		+	[[Category: McKee, K]]
		+	[[Category: Navis, M]]
		+	[[Category: Phad, G]]
		+	[[Category: Soldemo, M]]
		+	[[Category: Sundling, C]]
		+	[[Category: Tran, K]]
		+	[[Category: Wilson, R]]
		+	[[Category: Wyatt, R T]]
		+	[[Category: Fab fragment]]
		+	[[Category: Hiv viral envelope glycoprotein neutralization]]
		+	[[Category: Immune system]]

OCA at 07:28, 23 April 2014

2014-04-23T07:28:43Z

←Older revision		Revision as of 07:28, 23 April 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4q2z is ON HOLD	+	The entry 4q2z is ON HOLD until Paper Publication

	Authors: Navis, M., Tran, K., Bale, S., Phad, G., Guenaga, J., Wilson, R., Soldemo, M., McKee, K., Sundling, C., Mascola, J., Li, Y., Wyatt, R.T., Hedestam, G.B.K.		Authors: Navis, M., Tran, K., Bale, S., Phad, G., Guenaga, J., Wilson, R., Soldemo, M., McKee, K., Sundling, C., Mascola, J., Li, Y., Wyatt, R.T., Hedestam, G.B.K.

	Description: Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate		Description: Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate

OCA: Protected "4q2z" [edit=sysop:move=sysop]

2014-04-16T09:11:49Z

Protected "4q2z" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:11, 16 April 2014

OCA: New page: '''Unreleased structure''' The entry 4q2z is ON HOLD Authors: Navis, M., Tran, K., Bale, S., Phad, G., Guenaga, J., Wilson, R., Soldemo, M., McKee, K., Sundling, C., Mascola, J., Li, Y....

2014-04-16T09:11:48Z

New page: '''Unreleased structure''' The entry 4q2z is ON HOLD Authors: Navis, M., Tran, K., Bale, S., Phad, G., Guenaga, J., Wilson, R., Soldemo, M., McKee, K., Sundling, C., Mascola, J., Li, Y....

New page

'''Unreleased structure'''

The entry 4q2z is ON HOLD

Authors: Navis, M., Tran, K., Bale, S., Phad, G., Guenaga, J., Wilson, R., Soldemo, M., McKee, K., Sundling, C., Mascola, J., Li, Y., Wyatt, R.T., Hedestam, G.B.K.

Description: Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate