6ojp - Revision history

OCA at 07:11, 11 October 2023

OCA — Wed, 11 Oct 2023 07:11:45 GMT

←Older revision		Revision as of 07:11, 11 October 2023
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	<StructureSection load='6ojp' size='340' side='right'caption='[[6ojp]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='6ojp' size='340' side='right'caption='[[6ojp]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ojp]] 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=6OJP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OJP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ojp]] 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=6OJP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OJP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7LP:(5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide'>7LP</scene>, <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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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]] 2.17Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">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=7LP:(5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide'>7LP</scene>, <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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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=6ojp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ojp OCA], [~~http~~://pdbe.org/6ojp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ojp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ojp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ojp 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=6ojp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ojp OCA], [https://pdbe.org/6ojp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ojp RCSB], [https://www.ebi.ac.uk/pdbsum/6ojp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ojp 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/CD1D1_MOUSE CD1D1_MOUSE] Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells.<ref>PMID:11754812</ref> <ref>PMID:16314439</ref> <ref>PMID:16007091</ref>
	<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 6ojp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ojp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
		+	*[[CD1\|CD1]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Bitra, A]]	+	[[Category: Bitra A]]
-	[[Category: Zajonc~~, D M]]~~	+	[[Category: Zajonc DM]]
-	~~[[Category: Glycolipid-antigen presentation]]~~	+
-	~~[[Category: Ig-fold]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Mhc-fold~~]]	+

OCA at 06:13, 10 October 2019

OCA — Thu, 10 Oct 2019 06:13:57 GMT

←Older revision		Revision as of 06:13, 10 October 2019
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	<StructureSection load='6ojp' size='340' side='right'caption='[[6ojp]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='6ojp' size='340' side='right'caption='[[6ojp]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ojp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ojp]] 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=6OJP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7LP:(5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide'>7LP</scene>, <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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7LP:(5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide'>7LP</scene>, <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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">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=6ojp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ojp OCA], [http://pdbe.org/6ojp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ojp RCSB], [http://www.ebi.ac.uk/pdbsum/6ojp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ojp 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=6ojp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ojp OCA], [http://pdbe.org/6ojp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ojp RCSB], [http://www.ebi.ac.uk/pdbsum/6ojp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ojp ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Bitra, A]]		[[Category: Bitra, A]]
	[[Category: Zajonc, D M]]		[[Category: Zajonc, D M]]

OCA at 05:56, 21 August 2019

OCA — Wed, 21 Aug 2019 05:56:51 GMT

←Older revision		Revision as of 05:56, 21 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ojp is ~~ON HOLD until Paper~~ Publication	+	==Structure of glycolipid alpha-GSA[8,6P] in complex with mouse CD1d==
		+	<StructureSection load='6ojp' size='340' side='right'caption='[[6ojp]], [[Resolution\|resolution]] 2.17Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ojp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7LP:(5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide'>7LP</scene>, <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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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=6ojp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ojp OCA], [http://pdbe.org/6ojp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ojp RCSB], [http://www.ebi.ac.uk/pdbsum/6ojp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ojp 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 ==
		+	Type I Natural Killer T (NKT) cells are a population of innate like T lymphocytes that rapidly respond to alpha-GalCer presented by CD1d, via the production of both pro and anti-inflammatory cytokines. While developing novel alpha-GalCer analogs that were meant to be utilized as potential adjuvants due to their production of pro-inflammatory cytokines (Th1 skewers), we generated alpha-galactosylsphingamides (alpha-GSA). Surprisingly, alpha-GSAs are not potent antigens in vivodespite their strong T-cell receptor (TCR)-binding affinities. Here, using surface plasmon resonance (SPR), antigen presentation assays, and X-ray crystallography (yielding crystal structures of 19 different binary [CD1d-glycolipid] or ternary [CD1d-glycolipid-TCR] complexes at resolutions between 1.67 and 2.85 A), we characterized the biochemical and structural details of alpha-GSA recognition by murine NKT cells. We identified a molecular switch within murine (m)CD1d that modulates NKT cell activation by alpha-GSAs. We found that the molecular switch involves a hydrogen bond interaction between Tyr-73 of mCD1d and the amide group oxygen of alpha-GSAs. We further established that the length of the acyl chain controls the positioning of the amide group with respect to the molecular switch and works synergistically with Tyr-73 to control NKT cell activity. In conclusion, our findings reveal important mechanistic insights into the presentation and recognition of glycolipids with polar moieties in an otherwise apolar milieu.These observations may inform the development alpha-GSAs as specific NKT cell antagonists to modulate immune responses.

-	~~Authors: Zajonc, D.M~~., ~~Bitra~~, A.	+	A molecular switch in mouse CD1d modulates natural killer T cell activation by alpha-galactosylsphingamides.,Wang J, Guillaume J, Janssens J, Remesh SG, Ying G, Bitra A, Van Calenbergh S, Zajonc DM J Biol Chem. 2019 Aug 7. pii: RA119.009963. doi: 10.1074/jbc.RA119.009963. PMID:31391251<ref>PMID:31391251</ref>

-	~~Description: Structure~~ of ~~glycolipid alpha~~-~~GSA[8,6P] in complex with mouse CD1d~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6ojp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bitra, A]]		[[Category: Bitra, A]]
-	[[Category: Zajonc, D.M]]	+	[[Category: Zajonc, D M]]
		+	[[Category: Glycolipid-antigen presentation]]
		+	[[Category: Ig-fold]]
		+	[[Category: Immune system]]
		+	[[Category: Mhc-fold]]

OCA at 07:07, 1 May 2019

OCA — Wed, 01 May 2019 07:07:32 GMT

←Older revision		Revision as of 07:07, 1 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: ~~Dirk~~, M.Z., Bitra, A.	+	Authors: Zajonc, D.M., Bitra, A.

	Description: Structure of glycolipid alpha-GSA[8,6P] in complex with mouse CD1d		Description: Structure of glycolipid alpha-GSA[8,6P] in complex with mouse CD1d
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Bitra, A]]		[[Category: Bitra, A]]
-	[[Category: ~~Dirk~~, M.Z]]	+	[[Category: Zajonc, D.M]]

OCA at 04:56, 24 April 2019

OCA — Wed, 24 Apr 2019 04:56:23 GMT

←Older revision		Revision as of 04:56, 24 April 2019
Line 5:		Line 5:
	Authors: Dirk, M.Z., Bitra, A.		Authors: Dirk, M.Z., Bitra, A.

-	Description: ~~STRUCTURE OF GLYCOLIPID~~ alpha-GSA[8,6P] ~~IN COMPLEX WITH MOUSE CD1D~~	+	Description: Structure of glycolipid alpha-GSA[8,6P] in complex with mouse CD1d
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Bitra, A]]		[[Category: Bitra, A]]
	[[Category: Dirk, M.Z]]		[[Category: Dirk, M.Z]]

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

OCA — Wed, 17 Apr 2019 04:18:39 GMT

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

←Older revision

Revision as of 04:18, 17 April 2019

OCA: New page: '''Unreleased structure''' The entry 6ojp is ON HOLD Authors: Dirk, M.Z., Bitra, A. Description: STRUCTURE OF GLYCOLIPID alpha-GSA[8,6P] IN COMPLEX WITH MOUSE CD1D [[Category: Unreleas...

OCA — Wed, 17 Apr 2019 04:18:37 GMT

New page: '''Unreleased structure''' The entry 6ojp is ON HOLD Authors: Dirk, M.Z., Bitra, A. Description: STRUCTURE OF GLYCOLIPID alpha-GSA[8,6P] IN COMPLEX WITH MOUSE CD1D [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 6ojp is ON HOLD

Authors: Dirk, M.Z., Bitra, A.

Description: STRUCTURE OF GLYCOLIPID alpha-GSA[8,6P] IN COMPLEX WITH MOUSE CD1D
[[Category: Unreleased Structures]]
[[Category: Bitra, A]]
[[Category: Dirk, M.Z]]