6k4z - Revision history

OCA at 10:26, 22 November 2023

OCA — Wed, 22 Nov 2023 10:26:39 GMT

←Older revision		Revision as of 10:26, 22 November 2023
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	<StructureSection load='6k4z' size='340' side='right'caption='[[6k4z]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='6k4z' size='340' side='right'caption='[[6k4z]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k4z]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K4Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k4z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K4Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NPA:2-(4-HYDROXY-3-NITROPHENYL)ACETIC+ACID'>NPA</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]] 1.65Å</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=6k4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4z OCA], [~~http~~://pdbe.org/6k4z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k4z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k4z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4z ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NPA:2-(4-HYDROXY-3-NITROPHENYL)ACETIC+ACID'>NPA</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=6k4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4z OCA], [https://pdbe.org/6k4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k4z RCSB], [https://www.ebi.ac.uk/pdbsum/6k4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4z 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 6k4z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6k4z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Azuma, T]]	+	[[Category: Azuma T]]
-	[[Category: Ito, N]]	+	[[Category: Ito N]]
-	[[Category: Nishiguchi, A]]	+	[[Category: Nishiguchi A]]
-	[[Category: Numoto, N]]	+	[[Category: Numoto N]]
-	[[Category: Oda, M]]	+	[[Category: Oda M]]
-	~~[[Category: Affinity maturation]]~~	+
-	~~[[Category: Antigen binding]]~~	+
-	~~[[Category: Conformational change]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Somatic hypermutation~~]]	+

OCA at 11:08, 2 October 2019

OCA — Wed, 02 Oct 2019 11:08:41 GMT

←Older revision		Revision as of 11:08, 2 October 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6k4z is ~~ON HOLD until Paper~~ Publication	+	==Single-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID==
		+	<StructureSection load='6k4z' size='340' side='right'caption='[[6k4z]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6k4z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K4Z FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NPA:2-(4-HYDROXY-3-NITROPHENYL)ACETIC+ACID'>NPA</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6k4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4z OCA], [http://pdbe.org/6k4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4z RCSB], [http://www.ebi.ac.uk/pdbsum/6k4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4z ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Antibodies possessing high affinity and specificity are desired as therapeutic reagents and biosensor materials. Such antibodies are often obtained from immunized animals through the process referred to as affinity maturation where antibody affinity increases with time after immunization. Somatic hypermutation (SHM) was shown to be involved in this process; however, structural basis of affinity maturation has not well been understood yet. We analyzed the crystal structure of a high affinity anti-(4-hydroxy-3-nitrophenyl)acetyl antibody, C6, possessing Gly at position 95 of heavy chain and 17 amino acid replacements by SHM. Here, we discuss how the amino acid residues at position 95, introduced at a junction of VH and DH gene segments during gene-recombination, as well as those replaced by SHM contribute to increasing the affinity by comparing the C6 structure with that of a germline low affinity antibody, N1G9, possessing Tyr at position 95.

-	~~Authors: Nishiguchi~~, A., Numoto, N., Ito, N., Azuma, T., Oda, M.	+	Three-dimensional structure of a high affinity anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain.,Nishiguchi A, Numoto N, Ito N, Azuma T, Oda M Mol Immunol. 2019 Sep 11;114:545-552. doi: 10.1016/j.molimm.2019.09.001. PMID:31521018<ref>PMID:31521018</ref>

-	~~Description: Single-chain Fv antibody~~ of ~~C6 COMPLEXED WITH 2~~-(4-~~HYDROXY-3-NITROPHENYL)ACETIC ACID~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6k4z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Azuma, T]]		[[Category: Azuma, T]]
		+	[[Category: Ito, N]]
		+	[[Category: Nishiguchi, A]]
	[[Category: Numoto, N]]		[[Category: Numoto, N]]
	[[Category: Oda, M]]		[[Category: Oda, M]]
-	[[Category: ~~Nishiguchi, A~~]]	+	[[Category: Affinity maturation]]
-	[[Category: ~~Ito, N~~]]	+	[[Category: Antigen binding]]
		+	[[Category: Conformational change]]
		+	[[Category: Immune system]]
		+	[[Category: Somatic hypermutation]]

OCA: Protected "6k4z" [edit=sysop:move=sysop]

OCA — Wed, 05 Jun 2019 20:59:44 GMT

Protected "6k4z" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:59, 5 June 2019

OCA: New page: '''Unreleased structure''' The entry 6k4z is ON HOLD until Paper Publication Authors: Nishiguchi, A., Numoto, N., Ito, N., Azuma, T., Oda, M. Description: Single-chain Fv antibody of C...

OCA — Wed, 05 Jun 2019 20:59:42 GMT

New page: '''Unreleased structure''' The entry 6k4z is ON HOLD until Paper Publication Authors: Nishiguchi, A., Numoto, N., Ito, N., Azuma, T., Oda, M. Description: Single-chain Fv antibody of C...

New page

'''Unreleased structure'''

The entry 6k4z is ON HOLD until Paper Publication

Authors: Nishiguchi, A., Numoto, N., Ito, N., Azuma, T., Oda, M.

Description: Single-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID
[[Category: Unreleased Structures]]
[[Category: Azuma, T]]
[[Category: Numoto, N]]
[[Category: Oda, M]]
[[Category: Nishiguchi, A]]
[[Category: Ito, N]]