5fkp - Revision history

OCA at 06:55, 19 July 2023

OCA — Wed, 19 Jul 2023 06:55:30 GMT

←Older revision		Revision as of 06:55, 19 July 2023
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	<StructureSection load='5fkp' size='340' side='right'caption='[[5fkp]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5fkp' size='340' side='right'caption='[[5fkp]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fkp]] is a 3 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=5FKP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FKP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fkp]] is a 3 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=5FKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FKP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6UL:TETRACOSYL+PALMITATE'>6UL</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=TAR:D(-)-TARTARIC+ACID'>TAR</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]] 1.8Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5fkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fkp OCA], [~~http~~://pdbe.org/5fkp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fkp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fkp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fkp ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6UL:TETRACOSYL+PALMITATE'>6UL</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=TAR:D(-)-TARTARIC+ACID'>TAR</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=5fkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fkp OCA], [https://pdbe.org/5fkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fkp RCSB], [https://www.ebi.ac.uk/pdbsum/5fkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fkp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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> ~~[[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 21:		Line 22:
	==See Also==		==See Also==
	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]		*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
		+	*[[CD1\|CD1]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Girardi, E]]	+	[[Category: Girardi E]]
-	[[Category: Wang, J]]	+	[[Category: Wang J]]
-	[[Category: Zajonc~~, D M]]~~	+	[[Category: Zajonc DM]]
-	~~[[Category: Alpha-helical]]~~	+
-	~~[[Category: Antigen presentation]]~~	+
-	~~[[Category: Cd1d]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 07:24, 6 May 2020

OCA — Wed, 06 May 2020 07:24:13 GMT

←Older revision		Revision as of 07:24, 6 May 2020
Line 1:		Line 1:

	==Crystal structure of the mouse CD1d in complex with the p99 peptide==		==Crystal structure of the mouse CD1d in complex with the p99 peptide==
-	<StructureSection load='5fkp' size='340' side='right' caption='[[5fkp]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5fkp' size='340' side='right'caption='[[5fkp]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fkp]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FKP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FKP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fkp]] is a 3 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=5FKP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FKP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6UL:TETRACOSYL+PALMITATE'>6UL</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=~~GOL~~:~~GLYCEROL~~'>~~GOL~~</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL-D-GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~TAR~~:D~~(-)~~-~~TARTARIC+ACID~~'>~~TAR~~</scene>, <scene name='pdbligand=~~FUC~~:~~ALPHA~~-L-~~FUCOSE~~'>~~FUC~~</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA-~~D-~~MANNOSE~~'>~~MAN~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6UL:TETRACOSYL+PALMITATE'>6UL</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=TAR:D(-)-TARTARIC+ACID'>TAR</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=5fkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fkp OCA], [http://pdbe.org/5fkp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fkp RCSB], [http://www.ebi.ac.uk/pdbsum/5fkp PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5fkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fkp OCA], [http://pdbe.org/5fkp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fkp RCSB], [http://www.ebi.ac.uk/pdbsum/5fkp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fkp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5fkp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fkp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Girardi, E]]		[[Category: Girardi, E]]
	[[Category: Wang, J]]		[[Category: Wang, J]]

OCA at 17:04, 10 May 2016

OCA — Tue, 10 May 2016 17:04:53 GMT

←Older revision		Revision as of 17:04, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fkp is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the mouse CD1d in complex with the p99 peptide==
		+	<StructureSection load='5fkp' size='340' side='right' caption='[[5fkp]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fkp]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FKP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6UL:TETRACOSYL+PALMITATE'>6UL</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=5fkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fkp OCA], [http://pdbe.org/5fkp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fkp RCSB], [http://www.ebi.ac.uk/pdbsum/5fkp PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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> [[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 ==
		+	Mouse CD1d is a non-classical MHC molecule able to present lipids and glycolipids to a specialized subset of T cells known as Natural Killer T (NKT) cells. The antigens presented by CD1d has been shown to cover a broad range of chemical structures and to follow precise rules determining the potency of the antigen in the context of T cell activation. Together with lipids, initial reports suggested that CD1d can also bind and present hydrophobic peptides with a motif of the nature [FW]-X-X-[ILM]-X-X-W. However, the exact location of peptide binding and the molecular basis for the required motif are currently unknown. Here we present the crystal structure of the first peptide identified to bind CD1d, p99, and show that it binds in the antigen-binding groove of CD1d in a manner compatible with its presentation to T cell receptors. Interestingly, the peptide adopts an alpha-helical conformation, which orients the motif residues toward its deep binding groove, therefore explaining the molecular requirements for peptide binding. Moreover, we demonstrate that a lipopeptide version of the same peptide is able to bind CD1d in a similar conformation, identifying another class of molecules binding this antigen-presenting molecule.

-	~~Authors: Girardi~~, E., Wang, J., Zajonc~~, D~~.M.	+	Structure of an alpha-helical peptide and lipopeptide bound to the non-classical MHC class I molecule CD1d.,Girardi E, Wang J, Zajonc DM J Biol Chem. 2016 Mar 22. pii: jbc.M115.702118. PMID:27006394<ref>PMID:27006394</ref>

-	~~Description: Crystal structure~~ of the ~~mouse CD1d in complex with the p99 peptide~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5fkp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Girardi, E]]		[[Category: Girardi, E]]
	[[Category: Wang, J]]		[[Category: Wang, J]]
-	[[Category: Zajonc, D.M]]	+	[[Category: Zajonc, D M]]
		+	[[Category: Alpha-helical]]
		+	[[Category: Antigen presentation]]
		+	[[Category: Cd1d]]
		+	[[Category: Immune system]]

OCA: Protected "5fkp" [edit=sysop:move=sysop]

OCA — Tue, 01 Dec 2015 03:31:12 GMT

Protected "5fkp" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:31, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fkp is ON HOLD until Paper Publication Authors: Girardi, E., Wang, J., Zajonc, D.M. Description: Crystal structure of the mouse CD1d in complex wi...

OCA — Tue, 01 Dec 2015 03:31:11 GMT

New page: '''Unreleased structure''' The entry 5fkp is ON HOLD until Paper Publication Authors: Girardi, E., Wang, J., Zajonc, D.M. Description: Crystal structure of the mouse CD1d in complex wi...

New page

'''Unreleased structure'''

The entry 5fkp is ON HOLD until Paper Publication

Authors: Girardi, E., Wang, J., Zajonc, D.M.

Description: Crystal structure of the mouse CD1d in complex with the p99 peptide
[[Category: Unreleased Structures]]
[[Category: Girardi, E]]
[[Category: Wang, J]]
[[Category: Zajonc, D.M]]