5uem - Revision history

OCA at 13:26, 4 October 2023

OCA — Wed, 04 Oct 2023 13:26:21 GMT

←Older revision		Revision as of 13:26, 4 October 2023
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	<StructureSection load='5uem' size='340' side='right'caption='[[5uem]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5uem' size='340' side='right'caption='[[5uem]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uem]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~9hiv1 9hiv1~~] and [~~http~~://en.wikipedia.org/wiki/Human ~~Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UEM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5UEM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uem]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UEM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA~~-D-~~MANNOSE~~'>~~MAN~~</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]] 2.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uel\|5uel]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 Env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])~~</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=5uem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uem OCA], [https://pdbe.org/5uem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uem RCSB], [https://www.ebi.ac.uk/pdbsum/5uem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uem ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5uem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uem OCA], [~~http~~://pdbe.org/5uem PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5uem RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5uem PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5uem ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0M3KKW9_9HIV1 A0A0M3KKW9_9HIV1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human]]	+	[[Category: Homo sapiens]]
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bjorkman~~, P J~~]]	+	[[Category: Bjorkman PJ]]
-	[[Category: Gristick~~, H B~~]]	+	[[Category: Gristick HB]]
-	[[Category: Sievers~~, S A]]~~	+	[[Category: Sievers SA]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Envelope protein]]~~	+
-	~~[[Category: Hiv]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immunity~~]]	+

OCA at 12:34, 23 September 2020

OCA — Wed, 23 Sep 2020 12:34:39 GMT

←Older revision		Revision as of 12:34, 23 September 2020
Line 1:		Line 1:

	==Crystal structure of 354NC37 Fab in complex with HIV-1 clade AE strain 93TH057 gp120==		==Crystal structure of 354NC37 Fab in complex with HIV-1 clade AE strain 93TH057 gp120==
-	<StructureSection load='5uem' size='340' side='right' caption='[[5uem]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5uem' size='340' side='right'caption='[[5uem]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uem]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UEM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca.weizmann~~.~~ac.il/oca-docs~~/fgij/fg.htm?mol=5UEM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uem]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UEM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5UEM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA~~-D-~~MANNOSE~~'>~~MAN~~</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uel\|5uel]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uel\|5uel]]</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=5uem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uem OCA], [http://pdbe.org/5uem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uem RCSB], [http://www.ebi.ac.uk/pdbsum/5uem PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uem ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 Env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5uem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uem OCA], [http://pdbe.org/5uem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uem RCSB], [http://www.ebi.ac.uk/pdbsum/5uem PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uem ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5uem" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5uem" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Gp120 3D structures\|Gp120 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bjorkman, P J]]		[[Category: Bjorkman, P J]]
	[[Category: Gristick, H B]]		[[Category: Gristick, H B]]

OCA at 08:27, 10 January 2018

OCA — Wed, 10 Jan 2018 08:27:15 GMT

←Older revision		Revision as of 08:27, 10 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5uem is ~~ON HOLD~~	+	==Crystal structure of 354NC37 Fab in complex with HIV-1 clade AE strain 93TH057 gp120==
		+	<StructureSection load='5uem' size='340' side='right' caption='[[5uem]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5uem]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UEM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uel\|5uel]]</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=5uem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uem OCA], [http://pdbe.org/5uem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uem RCSB], [http://www.ebi.ac.uk/pdbsum/5uem PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uem ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Some HIV-1-infected patients develop broad and potent HIV-1 neutralizing antibodies (bNAbs) that when passively transferred to mice or macaques can treat or prevent infection. However, bNAbs typically fail to neutralize coexisting autologous viruses due to antibody-mediated selection against sensitive viral strains. We describe an HIV-1 controller expressing HLA-B5701 and HLA-B2705 who maintained low viral loads for 30 years after infection and developed broad and potent serologic activity against HIV-1. Neutralization was attributed to three different bNAbs targeting nonoverlapping sites on the HIV-1 envelope trimer (Env). One of the three, BG18, an antibody directed against the glycan-V3 portion of Env, is the most potent member of this class reported to date and, as revealed by crystallography and electron microscopy, recognizes HIV-1 Env in a manner that is distinct from other bNAbs in this class. Single-genome sequencing of HIV-1 from serum samples obtained over a period of 9 years showed a diverse group of circulating viruses, 88.5% (31 of 35) of which remained sensitive to at least one of the temporally coincident autologous bNAbs and the individual's serum. Thus, bNAb-sensitive strains of HIV-1 coexist with potent neutralizing antibodies that target the virus and may contribute to control in this individual. When administered as a mix, the three bNAbs controlled viremia in HIV-1YU2-infected humanized mice. Our finding suggests that combinations of bNAbs may contribute to control of HIV-1 infection.

-	~~Authors:~~ Sievers, S.A., Gristick, ~~H.B.~~, Bjorkman, P.J.	+	Coexistence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller.,Freund NT, Wang H, Scharf L, Nogueira L, Horwitz JA, Bar-On Y, Golijanin J, Sievers SA, Sok D, Cai H, Cesar Lorenzi JC, Halper-Stromberg A, Toth I, Piechocka-Trocha A, Gristick HB, van Gils MJ, Sanders RW, Wang LX, Seaman MS, Burton DR, Gazumyan A, Walker BD, West AP Jr, Bjorkman PJ, Nussenzweig MC Sci Transl Med. 2017 Jan 18;9(373). pii: eaal2144. doi:, 10.1126/scitranslmed.aal2144. PMID:28100831<ref>PMID:28100831</ref>

-	~~Description: Crystal structure~~ of ~~354NC37 Fab in complex with HIV~~-~~1 clade AE strain 93TH057 gp120~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Gristick, H.B]]	+	<div class="pdbe-citations 5uem" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Bjorkman~~, ~~P.J~~]]	+	== References ==
-	[[Category: ~~Sievers, S.A~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bjorkman, P J]]
		+	[[Category: Gristick, H B]]
		+	[[Category: Sievers, S A]]
		+	[[Category: Antibody]]
		+	[[Category: Envelope protein]]
		+	[[Category: Hiv]]
		+	[[Category: Immune system]]
		+	[[Category: Immunity]]

OCA at 13:37, 27 September 2017

OCA — Wed, 27 Sep 2017 13:37:34 GMT

←Older revision		Revision as of 13:37, 27 September 2017
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Gristick, H.B]]		[[Category: Gristick, H.B]]
-	[[Category: Sievers, S.A]]
	[[Category: Bjorkman, P.J]]		[[Category: Bjorkman, P.J]]
		+	[[Category: Sievers, S.A]]

OCA at 18:59, 15 March 2017

OCA — Wed, 15 Mar 2017 18:59:07 GMT

←Older revision		Revision as of 18:59, 15 March 2017
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Gristick, H.B]]		[[Category: Gristick, H.B]]
-	[[Category: Bjorkman, P.J]]
	[[Category: Sievers, S.A]]		[[Category: Sievers, S.A]]
		+	[[Category: Bjorkman, P.J]]

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

OCA — Wed, 18 Jan 2017 14:45:52 GMT

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

←Older revision

Revision as of 14:45, 18 January 2017

OCA: New page: '''Unreleased structure''' The entry 5uem is ON HOLD Authors: Sievers, S.A., Gristick, H.B., Bjorkman, P.J. Description: Crystal structure of 354NC37 Fab in complex with HIV-1 clade AE...

OCA — Wed, 18 Jan 2017 14:45:50 GMT

New page: '''Unreleased structure''' The entry 5uem is ON HOLD Authors: Sievers, S.A., Gristick, H.B., Bjorkman, P.J. Description: Crystal structure of 354NC37 Fab in complex with HIV-1 clade AE...

New page

'''Unreleased structure'''

The entry 5uem is ON HOLD

Authors: Sievers, S.A., Gristick, H.B., Bjorkman, P.J.

Description: Crystal structure of 354NC37 Fab in complex with HIV-1 clade AE strain 93TH057 gp120
[[Category: Unreleased Structures]]
[[Category: Gristick, H.B]]
[[Category: Bjorkman, P.J]]
[[Category: Sievers, S.A]]