7ri1 - Revision history

OCA at 09:27, 25 October 2023

OCA — Wed, 25 Oct 2023 09:27:56 GMT

←Older revision		Revision as of 09:27, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7ri1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RI1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ri1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RI1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.55Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ri1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ri1 OCA], [https://pdbe.org/7ri1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ri1 RCSB], [https://www.ebi.ac.uk/pdbsum/7ri1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ri1 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=7ri1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ri1 OCA], [https://pdbe.org/7ri1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ri1 RCSB], [https://www.ebi.ac.uk/pdbsum/7ri1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ri1 ProSAT]</span></td></tr>
	</table>		</table>
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	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Gp120 3D structures\|Gp120 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:06, 1 February 2023

OCA — Wed, 01 Feb 2023 12:06:23 GMT

←Older revision		Revision as of 12:06, 1 February 2023
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	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/R4GRV3_9HIV1 R4GRV3_9HIV1]]	+	[https://www.uniprot.org/uniprot/R4GRV3_9HIV1 R4GRV3_9HIV1]
	<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 7ri1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7ri1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:52, 8 September 2022

OCA — Thu, 08 Sep 2022 03:52:14 GMT

←Older revision		Revision as of 03:52, 8 September 2022
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-	====	+	==Crystal structure of anti-HIV llama VHH antibody J3 in complex with HIV-1 C1086 gp120==
-	<StructureSection load='7ri1' size='340' side='right'caption='[[7ri1]]' scene=''>	+	<StructureSection load='7ri1' size='340' side='right'caption='[[7ri1]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ri1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RI1 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=7ri1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ri1 OCA], [https://pdbe.org/7ri1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ri1 RCSB], [https://www.ebi.ac.uk/pdbsum/7ri1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ri1 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ri1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ri1 OCA], [https://pdbe.org/7ri1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ri1 RCSB], [https://www.ebi.ac.uk/pdbsum/7ri1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ri1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/R4GRV3_9HIV1 R4GRV3_9HIV1]]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nanobodies can achieve remarkable neutralization of genetically diverse pathogens, including HIV-1. To gain insight into their recognition, we determined crystal structures of four llama nanobodies (J3, A12, C8, and D7), all of which targeted the CD4-binding site, in complex with the HIV-1 envelope (Env) gp120 core, and determined a cryoelectron microscopy (cryo-EM) structure of J3 with the Env trimer. Crystal and cryo-EM structures of J3 complexes revealed this nanobody to mimic binding to the prefusion-closed trimer for the primary site of CD4 recognition as well as a secondary quaternary site. In contrast, crystal structures of A12, C8, and D7 with gp120 revealed epitopes that included portions of the gp120 inner domain, inaccessible on the prefusion-closed trimer. Overall, these structures explain the broad and potent neutralization of J3 and limited neutralization of A12, C8, and D7, which utilized binding modes incompatible with the neutralization-targeted prefusion-closed conformation of Env.
		+
		+	Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site.,Zhou T, Chen L, Gorman J, Wang S, Kwon YD, Lin BC, Louder MK, Rawi R, Stancofski ED, Yang Y, Zhang B, Quigley AF, McCoy LE, Rutten L, Verrips T, Weiss RA, Doria-Rose NA, Shapiro L, Kwong PD Structure. 2022 Jun 2;30(6):862-875.e4. doi: 10.1016/j.str.2022.03.012. Epub 2022, Apr 11. PMID:35413243<ref>PMID:35413243</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ri1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human immunodeficiency virus 1]]
		+	[[Category: Lama glama]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Kwong PD]]
		+	[[Category: Zhou T]]

OCA at 10:46, 30 March 2022

OCA — Wed, 30 Mar 2022 10:46:12 GMT

←Older revision		Revision as of 10:46, 30 March 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7ri1 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7ri1' size='340' side='right'caption='[[7ri1]]' scene=''>
-	~~Authors~~: ~~Zhou, T~~.~~, Kwong, P~~.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of anti~~-~~HIV llama VHH antibody A12 in complex with HIV-1 C1086 gp120~~	+	</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=7ri1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ri1 OCA], [https://pdbe.org/7ri1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ri1 RCSB], [https://www.ebi.ac.uk/pdbsum/7ri1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ri1 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Kwong, P.D~~]]	+	__TOC__
-	[[Category: ~~Zhou, T~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 07:40, 8 September 2021

OCA — Wed, 08 Sep 2021 07:40:05 GMT

←Older revision		Revision as of 07:40, 8 September 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ri1 is ON HOLD	+	The entry 7ri1 is ON HOLD until Paper Publication

	Authors: Zhou, T., Kwong, P.D.		Authors: Zhou, T., Kwong, P.D.

OCA: Protected "7ri1" [edit=sysop:move=sysop]

OCA — Wed, 28 Jul 2021 09:36:30 GMT

Protected "7ri1" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:36, 28 July 2021

OCA: New page: '''Unreleased structure''' The entry 7ri1 is ON HOLD Authors: Zhou, T., Kwong, P.D. Description: Crystal structure of anti-HIV llama VHH antibody A12 in complex with HIV-1 C1086 gp120 ...

OCA — Wed, 28 Jul 2021 09:36:29 GMT

New page: '''Unreleased structure''' The entry 7ri1 is ON HOLD Authors: Zhou, T., Kwong, P.D. Description: Crystal structure of anti-HIV llama VHH antibody A12 in complex with HIV-1 C1086 gp120 ...

New page

'''Unreleased structure'''

The entry 7ri1 is ON HOLD

Authors: Zhou, T., Kwong, P.D.

Description: Crystal structure of anti-HIV llama VHH antibody A12 in complex with HIV-1 C1086 gp120
[[Category: Unreleased Structures]]
[[Category: Kwong, P.D]]
[[Category: Zhou, T]]