6tyb - Revision history

OCA at 07:40, 11 October 2023

OCA — Wed, 11 Oct 2023 07:40:14 GMT

←Older revision		Revision as of 07:40, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6tyb' size='340' side='right'caption='[[6tyb]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6tyb' size='340' side='right'caption='[[6tyb]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tyb]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Civ Civ~~] and [~~http~~://en.wikipedia.org/wiki/~~Macmu Macmu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TYB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6TYB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tyb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Macaca_mulatta Macaca mulatta] and [https://en.wikipedia.org/wiki/Simian_immunodeficiency_virus Simian immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TYB 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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.301Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11723 CIV]), CD4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9544 MACMU])</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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6tyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tyb OCA], [~~http~~://pdbe.org/6tyb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tyb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tyb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tyb 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=6tyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tyb OCA], [https://pdbe.org/6tyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tyb RCSB], [https://www.ebi.ac.uk/pdbsum/6tyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tyb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E7CWP5_SIV E7CWP5_SIV]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6tyb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6tyb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[CD4 3D structures\|CD4 3D structures]]
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Civ]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Macmu~~]]	+	[[Category: Macaca mulatta]]
-	[[Category: ~~Gorman, J~~]]	+	[[Category: Simian immunodeficiency virus]]
-	[[Category: ~~Kwong, P D~~]]	+	[[Category: Gorman J]]
-	[[Category: ~~Bnab]]~~	+	[[Category: Kwong PD]]
-	~~[[Category: Fab]]~~	+
-	~~[[Category: Glycan]]~~	+
-	~~[[Category: Gp120]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 08:16, 23 October 2019

OCA — Wed, 23 Oct 2019 08:16:26 GMT

←Older revision		Revision as of 08:16, 23 October 2019
Line 3:		Line 3:
	<StructureSection load='6tyb' size='340' side='right'caption='[[6tyb]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6tyb' size='340' side='right'caption='[[6tyb]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tyb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TYB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TYB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tyb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Civ Civ] and [http://en.wikipedia.org/wiki/Macmu Macmu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TYB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TYB 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=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"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</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">env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11723 CIV]), CD4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9544 MACMU])</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=6tyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tyb OCA], [http://pdbe.org/6tyb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tyb RCSB], [http://www.ebi.ac.uk/pdbsum/6tyb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tyb 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=6tyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tyb OCA], [http://pdbe.org/6tyb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tyb RCSB], [http://www.ebi.ac.uk/pdbsum/6tyb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tyb ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	HIV- and SIV-envelope (Env) trimers are both extensively glycosylated, and antibodies identified to date have been unable to fully neutralize SIVmac239. Here, we report the isolation, structure, and glycan interactions of antibody ITS90.03, a monoclonal antibody that completely neutralized the highly neutralization-resistant isolate, SIVmac239. The co-crystal structure of a fully glycosylated SIVmac239-gp120 core in complex with rhesus CD4 and the antigen-binding fragment of ITS90.03 at 2.5-A resolution revealed that ITS90 recognized an epitope comprised of 45% glycan. SIV-gp120 core, rhesus CD4, and their complex could each be aligned structurally to their human counterparts. The structure revealed that glycans masked most of the SIV Env protein surface, with ITS90 targeting a glycan hole, which is occupied in approximately 83% of SIV strains by glycan N238. Overall, the SIV glycan shield appears to functionally resemble its HIV counterpart in coverage of spike, shielding from antibody, and modulation of receptor accessibility.
		+
		+	Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields.,Gorman J, Mason RD, Nettey L, Cavett N, Chuang GY, Peng D, Tsybovsky Y, Verardi R, Nguyen R, Ambrozak D, Biris K, LaBranche CC, Ramesh A, Schramm CA, Zhou J, Bailer RT, Kepler TB, Montefiori DC, Shapiro L, Douek DC, Mascola JR, Roederer M, Kwong PD Immunity. 2019 Oct 15;51(4):724-734.e4. doi: 10.1016/j.immuni.2019.09.007. Epub, 2019 Oct 2. PMID:31586542<ref>PMID:31586542</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6tyb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Civ]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Macmu]]
	[[Category: Gorman, J]]		[[Category: Gorman, J]]
	[[Category: Kwong, P D]]		[[Category: Kwong, P D]]

OCA at 10:44, 2 October 2019

OCA — Wed, 02 Oct 2019 10:44:06 GMT

←Older revision		Revision as of 10:44, 2 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6tyb ~~is ON HOLD~~	+	==Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields==
-		+	<StructureSection load='6tyb' size='340' side='right'caption='[[6tyb]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~Authors~~: ~~Gorman, J~~.~~, Kwong, P~~.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6tyb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TYB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TYB FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure of Glycosylated SIVmac239 gp120 Core in Complex with Rhesus CD4 and Neutralizing Antibody ITS90~~.~~03 at 2~~.~~5 A Resolution~~	+	</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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=6tyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tyb OCA], [http://pdbe.org/6tyb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tyb RCSB], [http://www.ebi.ac.uk/pdbsum/6tyb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tyb ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Kwong~~, P.D]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Gorman, J]]		[[Category: Gorman, J]]
		+	[[Category: Kwong, P D]]
		+	[[Category: Bnab]]
		+	[[Category: Fab]]
		+	[[Category: Glycan]]
		+	[[Category: Gp120]]
		+	[[Category: Immune system]]

OCA: Protected "6tyb" [edit=sysop:move=sysop]

OCA — Wed, 14 Aug 2019 15:16:40 GMT

Protected "6tyb" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:16, 14 August 2019

OCA: New page: '''Unreleased structure''' The entry 6tyb is ON HOLD Authors: Gorman, J., Kwong, P.D. Description: Crystal Structure of Glycosylated SIVmac239 gp120 Core in Complex with Rhesus CD4 and...

OCA — Wed, 14 Aug 2019 15:16:38 GMT

New page: '''Unreleased structure''' The entry 6tyb is ON HOLD Authors: Gorman, J., Kwong, P.D. Description: Crystal Structure of Glycosylated SIVmac239 gp120 Core in Complex with Rhesus CD4 and...

New page

'''Unreleased structure'''

The entry 6tyb is ON HOLD

Authors: Gorman, J., Kwong, P.D.

Description: Crystal Structure of Glycosylated SIVmac239 gp120 Core in Complex with Rhesus CD4 and Neutralizing Antibody ITS90.03 at 2.5 A Resolution
[[Category: Unreleased Structures]]
[[Category: Kwong, P.D]]
[[Category: Gorman, J]]