6c5j - Revision history

OCA at 14:56, 4 October 2023

2023-10-04T14:56:26Z

←Older revision		Revision as of 14:56, 4 October 2023
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	<StructureSection load='6c5j' size='340' side='right'caption='[[6c5j]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='6c5j' size='340' side='right'caption='[[6c5j]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c5j]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C5J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6C5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c5j]] 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=6C5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C5J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GP1:GLUCOSAMINE+1-PHOSPHATE'>GP1</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</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]] 2.29Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6c5h\|6c5h]], [[6c5i\|6c5i]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GP1:GLUCOSAMINE+1-PHOSPHATE'>GP1</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</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=6c5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c5j OCA], [~~http~~://pdbe.org/6c5j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6c5j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6c5j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6c5j 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=6c5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c5j OCA], [https://pdbe.org/6c5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c5j RCSB], [https://www.ebi.ac.uk/pdbsum/6c5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c5j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q99LC4_MOUSE Q99LC4_MOUSE]
	<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 6c5j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6c5j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Evans~~, S V~~]]	+	[[Category: Evans SV]]
-	[[Category: Haji-Ghassemi, O]]	+	[[Category: Haji-Ghassemi O]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Antigen]]~~	+
-	~~[[Category: Carbohydrate]]~~	+
-	~~[[Category: Chlamydia]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Lipopolysaccharide]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 08:40, 8 January 2020

2020-01-08T08:40:35Z

←Older revision		Revision as of 08:40, 8 January 2020
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	==S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1)==		==S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1)==
-	<StructureSection load='6c5j' size='340' side='right' caption='[[6c5j]], [[Resolution\|resolution]] 2.29Å' scene=''>	+	<StructureSection load='6c5j' size='340' side='right'caption='[[6c5j]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6c5j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C5J FirstGlance]. <br>		<table><tr><td colspan='2'>[[6c5j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C5J FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Evans, S V]]		[[Category: Evans, S V]]

OCA at 06:34, 9 January 2019

2019-01-09T06:34:12Z

←Older revision		Revision as of 06:34, 9 January 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6c5j is ~~ON HOLD until Paper~~ Publication	+	==S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1)==
		+	<StructureSection load='6c5j' size='340' side='right' caption='[[6c5j]], [[Resolution\|resolution]] 2.29Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6c5j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C5J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GP1:GLUCOSAMINE+1-PHOSPHATE'>GP1</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6c5h\|6c5h]], [[6c5i\|6c5i]]</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=6c5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c5j OCA], [http://pdbe.org/6c5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c5j RCSB], [http://www.ebi.ac.uk/pdbsum/6c5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c5j ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Murine antibodies S25-23, S25-26 and S25-5 derive from a common germ-line origin and all bind the Chlamydiaceae family-specific epitope alphaKdo(2-->8)alphaKdo(2-->4)alphaKdo, (where Kdo is 3-deoxy-alpha-D-manno-oct-2-ulosonic acid) with high affinity and specificity. These antibodies recognize the entire trisaccharide antigen in a linkage dependent manner via a groove composed largely of germ-line residues. Despite sharing identical heavy and light chain genes, S25-23 binds the family-specific epitope with nanomolar affinity, which is an order of magnitude higher than S25-26, while S25-5 displays an affinity between that of S25-23 and S25-26. We determined the high resolution crystal structures of S25-23 and S25-5 antigen-binding fragments in complex with a pentasaccharide derived from the LPS of Chlamydia, and measured the affinity of S25-5 towards chlamydial LPS antigens using isothermal titration microcalorimetry. The 1.75 A resolution structure of S25-23 shows how subtle conservative mutations Arg(L)-27E to lysine and Ser(H)-56 to threonine lead to an order of magnitude increase in affinity. Importantly, comparison between previous S25-26 structures and the 1.99 and 2.05 A resolution liganded and unliganded structures of S25-5, respectively, shows how a Ser(L)-27E results in intermediate affinity due to reduced enthalpic penalty associated with complex formation that would otherwise be required for arginine in this position. This strategy allows for subtle adjustments in combining site via affinity maturation to lead to dramatic consequences in affinity of an antibody for its antigen.

-	~~Authors:~~ Haji-Ghassemi, O~~., Evans~~, S.V.	+	Subtle changes in the combining site of the Chlamydiaceae-specific mAb S25-23 increase antibody-carbohydrate binding affinity by an order of magnitude.,Haji-Ghassemi O, Muller-Loennies S, Brooks CL, MacKenzie CR, Caveney N, Van Petegem F, Brade L, Kosma P, Brade H, Evans SV Biochemistry. 2018 Dec 20. doi: 10.1021/acs.biochem.8b00318. PMID:30571096<ref>PMID:30571096</ref>

-	~~Description: S25~~-~~23 Fab in complex with Chlamydiaceae LPS (Crystal form 1)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Evans, S.V]]	+	<div class="pdbe-citations 6c5j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Mus musculus]]
		+	[[Category: Evans, S V]]
	[[Category: Haji-Ghassemi, O]]		[[Category: Haji-Ghassemi, O]]
		+	[[Category: Antibody]]
		+	[[Category: Antigen]]
		+	[[Category: Carbohydrate]]
		+	[[Category: Chlamydia]]
		+	[[Category: Complex]]
		+	[[Category: Immune system]]
		+	[[Category: Lipopolysaccharide]]
		+	[[Category: Sugar binding protein]]

OCA at 04:46, 31 January 2018

2018-01-31T04:46:32Z

←Older revision		Revision as of 04:46, 31 January 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6c5j is ON HOLD	+	The entry 6c5j is ON HOLD until Paper Publication

	Authors: Haji-Ghassemi, O., Evans, S.V.		Authors: Haji-Ghassemi, O., Evans, S.V.

OCA: Protected "6c5j" [edit=sysop:move=sysop]

2018-01-24T17:20:24Z

Protected "6c5j" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:20, 24 January 2018

OCA: New page: '''Unreleased structure''' The entry 6c5j is ON HOLD Authors: Haji-Ghassemi, O., Evans, S.V. Description: S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1) [[Category: Unre...

2018-01-24T17:20:23Z

New page: '''Unreleased structure''' The entry 6c5j is ON HOLD Authors: Haji-Ghassemi, O., Evans, S.V. Description: S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1) [[Category: Unre...

New page

'''Unreleased structure'''

The entry 6c5j is ON HOLD

Authors: Haji-Ghassemi, O., Evans, S.V.

Description: S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1)
[[Category: Unreleased Structures]]
[[Category: Evans, S.V]]
[[Category: Haji-Ghassemi, O]]