6mjq - Revision history

OCA at 06:33, 11 October 2023

OCA — Wed, 11 Oct 2023 06:33:07 GMT

←Older revision		Revision as of 06:33, 11 October 2023
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	==Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex==		==Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex==
-	<StructureSection load='6mjq' size='340' side='right' caption='[[6mjq]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='6mjq' size='340' side='right'caption='[[6mjq]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mjq]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~] and [~~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=6MJQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MJQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mjq]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MJQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MJQ 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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JUD:N-{(2S,3S,4R)-3,4-dihydroxy-1-[(4-O-{[4-(trifluoromethyl)phenyl]methyl}-alpha-D-galactopyranosyl)oxy]octadecan-2-yl}hexacosanamide'>JUD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 3Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B2M, HDCMA22P ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), TRBC2, TCRBC2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), Cd1d1, mCG_3074 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), B2m ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JUD:N-{(2S,3S,4R)-3,4-dihydroxy-1-[(4-O-{[4-(trifluoromethyl)phenyl]methyl}-alpha-D-galactopyranosyl)oxy]octadecan-2-yl}hexacosanamide'>JUD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6mjq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mjq OCA], [~~http~~://pdbe.org/6mjq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mjq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mjq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mjq 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=6mjq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mjq OCA], [https://pdbe.org/6mjq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mjq RCSB], [https://www.ebi.ac.uk/pdbsum/6mjq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mjq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~B2MG_MOUSE B2MG_MOUSE~~]~~] Component of the class I major histocompatibility complex (MHC)~~. ~~Involved in the presentation of peptide antigens to the immune system~~.	+	[https://www.uniprot.org/uniprot/A0A0B4J1J9_MOUSE A0A0B4J1J9_MOUSE] [https://www.uniprot.org/uniprot/K7N5M3_HUMAN K7N5M3_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6mjq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6mjq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
		+	*[[CD1\|CD1]]
		+	*[[T-cell receptor 3D structures\|T-cell receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Bitra, A~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Janssens, J~~]]	+	[[Category: Bitra A]]
-	[[Category: ~~Zajonc, D M~~]]	+	[[Category: Janssens J]]
-	[[Category: ~~Glycolipid antigen presentation]]~~	+	[[Category: Zajonc DM]]
-	~~[[Category: Ig-fold]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immune system-inhibitor complex]]~~	+
-	~~[[Category: Mhc-fold]]~~	+
-	~~[[Category: T cell receptor~~]]	+

OCA at 12:42, 16 January 2019

OCA — Wed, 16 Jan 2019 12:42:10 GMT

←Older revision		Revision as of 12:42, 16 January 2019
Line 3:		Line 3:
	<StructureSection load='6mjq' size='340' side='right' caption='[[6mjq]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6mjq' size='340' side='right' caption='[[6mjq]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mjq]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MJQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mjq]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [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=6MJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MJQ 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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JUD:N-{(2S,3S,4R)-3,4-dihydroxy-1-[(4-O-{[4-(trifluoromethyl)phenyl]methyl}-alpha-D-galactopyranosyl)oxy]octadecan-2-yl}hexacosanamide'>JUD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JUD:N-{(2S,3S,4R)-3,4-dihydroxy-1-[(4-O-{[4-(trifluoromethyl)phenyl]methyl}-alpha-D-galactopyranosyl)oxy]octadecan-2-yl}hexacosanamide'>JUD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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">B2M, HDCMA22P ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), TRBC2, TCRBC2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), Cd1d1, mCG_3074 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), B2m ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=6mjq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mjq OCA], [http://pdbe.org/6mjq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mjq RCSB], [http://www.ebi.ac.uk/pdbsum/6mjq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mjq 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=6mjq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mjq OCA], [http://pdbe.org/6mjq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mjq RCSB], [http://www.ebi.ac.uk/pdbsum/6mjq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mjq ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Bitra, A]]		[[Category: Bitra, A]]
	[[Category: Janssens, J]]		[[Category: Janssens, J]]

OCA at 06:39, 9 January 2019

OCA — Wed, 09 Jan 2019 06:39:51 GMT

←Older revision		Revision as of 06:39, 9 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6mjq is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex==
		+	<StructureSection load='6mjq' size='340' side='right' caption='[[6mjq]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6mjq]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MJQ 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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JUD:N-{(2S,3S,4R)-3,4-dihydroxy-1-[(4-O-{[4-(trifluoromethyl)phenyl]methyl}-alpha-D-galactopyranosyl)oxy]octadecan-2-yl}hexacosanamide'>JUD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6mjq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mjq OCA], [http://pdbe.org/6mjq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mjq RCSB], [http://www.ebi.ac.uk/pdbsum/6mjq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mjq ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/B2MG_MOUSE B2MG_MOUSE]] Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Invariant natural killer T-cells (iNKT) are a glycolipid-responsive subset of T-lymphocytes that fulfill a pivotal role in the immune system. The archetypical synthetic glycolipid, alpha-galactosylceramide (alpha-GalCer), whose molecular framework is inspired by a group of amphiphilic natural products, remains the most studied antigen for iNKT-cells. Nonetheless, the potential of alpha-GalCer as an immunostimulating agent is compromised by the fact that this glycolipid elicits simultaneous secretion of Th1- and Th2-cytokines. This has incited medicinal chemistry efforts to identify analogues that are able to perturb the Th1/Th2 balance. In this work, we present the synthesis of an extensive set of 4"-O-alkylated alpha-GalCer analogues, which were evaluated in vivo for their cytokine induction. We have found that conversion of the 4"-OH group to ether moieties decreases the immunogenic potential in mice relative to alpha-GalCer. Yet, the benzyl-modified glycolipids are able to produce a distinct pro-inflammatory immune response. The crystal structures suggest an extra hydrophobic interaction between the benzyl moiety and the alpha2-helix of CD1d.

-	~~Authors~~: ~~Zajonc~~, ~~D.M~~., ~~Bitra~~, A., ~~Janssens~~, J.	+	4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies.,Janssens J, Bitra A, Wang J, Decruy T, Venken K, van der Eycken J, Elewaut D, Zajonc DM, van Calenbergh S ChemMedChem. 2019 Jan 8;14(1):147-168. doi: 10.1002/cmdc.201800649. Epub 2018 Dec, 17. PMID:30556652<ref>PMID:30556652</ref>

-	~~Description: Crystal structure~~ of the ~~mCD1d~~/~~xxp (JJ295) /iNKTCR ternary complex~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Janssens, J]]~~	+	<div class="pdbe-citations 6mjq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bitra, A]]		[[Category: Bitra, A]]
-	[[Category: Zajonc, D.M]]	+	[[Category: Janssens, J]]
		+	[[Category: Zajonc, D M]]
		+	[[Category: Glycolipid antigen presentation]]
		+	[[Category: Ig-fold]]
		+	[[Category: Immune system]]
		+	[[Category: Immune system-inhibitor complex]]
		+	[[Category: Mhc-fold]]
		+	[[Category: T cell receptor]]

OCA at 06:30, 17 October 2018

OCA — Wed, 17 Oct 2018 06:30:25 GMT

←Older revision		Revision as of 06:30, 17 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Zajonc, D.M., Bitra, A., Janssens, J.		Authors: Zajonc, D.M., Bitra, A., Janssens, J.

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

OCA — Wed, 03 Oct 2018 06:26:34 GMT

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

←Older revision

Revision as of 06:26, 3 October 2018

OCA: New page: '''Unreleased structure''' The entry 6mjq is ON HOLD Authors: Zajonc, D.M., Bitra, A., Janssens, J. Description: Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex [[Ca...

OCA — Wed, 03 Oct 2018 06:26:33 GMT

New page: '''Unreleased structure''' The entry 6mjq is ON HOLD Authors: Zajonc, D.M., Bitra, A., Janssens, J. Description: Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex [[Ca...

New page

'''Unreleased structure'''

The entry 6mjq is ON HOLD

Authors: Zajonc, D.M., Bitra, A., Janssens, J.

Description: Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex
[[Category: Unreleased Structures]]
[[Category: Janssens, J]]
[[Category: Bitra, A]]
[[Category: Zajonc, D.M]]