7km6 - Revision history

OCA at 15:28, 18 October 2023

OCA — Wed, 18 Oct 2023 15:28:04 GMT

←Older revision		Revision as of 15:28, 18 October 2023
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-	====	+	==APOBEC3B antibody 5G7 Fv-clasp==
-	<StructureSection load='7km6' size='340' side='right'caption='[[7km6]]' scene=''>	+	<StructureSection load='7km6' size='340' side='right'caption='[[7km6]], [[Resolution\|resolution]] 1.67Å' 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'>[[7km6]] is a 4 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=7KM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KM6 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=7km6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7km6 OCA], [https://pdbe.org/7km6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7km6 RCSB], [https://www.ebi.ac.uk/pdbsum/7km6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7km6 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]] 1.67Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7km6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7km6 OCA], [https://pdbe.org/7km6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7km6 RCSB], [https://www.ebi.ac.uk/pdbsum/7km6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7km6 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	APOBEC3B (A3B) is one of seven human APOBEC3 DNA cytosine deaminases that restrict viral infections as part of the overall innate immune response, but it also plays a major role in tumor evolution by mutating genomic DNA. Given the importance of A3B as a restriction factor of viral infections and as a driver of multiple human cancers, selective antibodies against A3B are highly desirable for its specific detection in various research and possibly diagnostic applications. Here, we describe a high-affinity minimal antibody, designated 5G7, obtained via a phage display screening against the C-terminal catalytic domain (ctd) of A3B. 5G7 also binds APOBEC3A that is highly homologous to A3Bctd but does not bind the catalytic domain of APOBEC3G, another Z1-type deaminase domain. The crystal structure of 5G7 shows a canonical arrangement of the heavy and light chain variable domains, with their complementarity-determining region (CDR) loops lining an antigen-binding cleft that accommodates a pair of alpha-helices. To understand the mechanism of A3Bctd recognition by 5G7, we used the crystal structures of A3Bctd and 5G7 as templates and computationally predicted the A3B-5G7 complex structure. Stable binding poses obtained by the simulation were further tested by site-directed mutagenesis and in vitro binding analyses. These studies mapped the epitope for 5G7 to a portion of C-terminal alpha6 helix of A3Bctd, with Arg374 playing an essential role. The same region of A3Bctd was used previously as a peptide antigen for generating a rabbit monoclonal antibody (mAb 5210-87-13), suggesting that this region is particularly immunogenic and that these antibodies from very different origins may share similar binding modes. Our studies provide a platform for the development of selective antibodies against A3B and other APOBEC3 family enzymes.
		+
		+	Structural Characterization of a Minimal Antibody against Human APOBEC3B.,Tang H, Demir O, Kurniawan F, Brown WL, Shi K, Moeller NH, Carpenter MA, Belica C, Orellana K, Du G, LeBeau AM, Amaro RE, Harris RS, Aihara H Viruses. 2021 Apr 12;13(4):663. doi: 10.3390/v13040663. PMID:33921405<ref>PMID:33921405</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7km6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Aihara H]]
		+	[[Category: Shi K]]
		+	[[Category: Tang H]]

OCA at 09:21, 12 May 2021

OCA — Wed, 12 May 2021 09:21:18 GMT

←Older revision		Revision as of 09:21, 12 May 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7km6 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7km6' size='340' side='right'caption='[[7km6]]' scene=''>
-	~~Authors~~:	+	== 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~~:	+	</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=7km6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7km6 OCA], [https://pdbe.org/7km6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7km6 RCSB], [https://www.ebi.ac.uk/pdbsum/7km6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7km6 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:35, 24 February 2021

OCA — Wed, 24 Feb 2021 05:35:59 GMT

←Older revision		Revision as of 05:35, 24 February 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7km6 is ON HOLD	+	The entry 7km6 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 08:40, 17 February 2021

OCA — Wed, 17 Feb 2021 08:40:24 GMT

←Older revision		Revision as of 08:40, 17 February 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7km6 is ON HOLD ~~until Paper Publication~~	+	The entry 7km6 is ON HOLD

	Authors:		Authors:

OCA at 11:10, 16 December 2020

OCA — Wed, 16 Dec 2020 11:10:31 GMT

←Older revision		Revision as of 11:10, 16 December 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7km6 is ON HOLD	+	The entry 7km6 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7km6" [edit=sysop:move=sysop]

OCA — Wed, 11 Nov 2020 06:33:58 GMT

Protected "7km6" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:33, 11 November 2020

OCA: New page: '''Unreleased structure''' The entry 7km6 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 11 Nov 2020 06:33:57 GMT

New page: '''Unreleased structure''' The entry 7km6 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7km6 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]