2akr: Difference between revisions

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==~~Structural basis of sulfatide presentation by mouse CD1d~~==

====

== Structural highlights ==

<table><tr><td colspan='2'>~~[[2akr]] is a 4 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=~~2AKR~~ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=~~2AKR~~ FirstGlance]. <br>

<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIS:(15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE'>CIS</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>

</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=2akr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2akr OCA], [https://pdbe.org/2akr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2akr RCSB], [https://www.ebi.ac.uk/pdbsum/2akr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2akr ProSAT]</span></td></tr>

<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cd1d1, Cd1.1 ([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=2akr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2akr OCA], [~~http~~://pdbe.org/2akr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2akr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2akr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2akr ProSAT]</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>

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

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Line 16:

</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2akr ConSurf].

~~<div style="background-color:#fffaf0;">~~

~~== Publication Abstract from PubMed ==~~

Sulfatide derived from the myelin stimulates a distinct population of CD1d-restricted natural killer T (NKT) cells. Cis-tetracosenoyl sulfatide is one of the immunodominant species in myelin as identified by proliferation, cytokine secretion, and CD1d tetramer staining. The crystal structure of mouse CD1d in complex with cis-tetracosenoyl sulfatide at 1.9 A resolution reveals that the longer cis-tetracosenoyl fatty acid chain fully occupies the A' pocket of the CD1d binding groove, whereas the sphingosine chain fills up the F' pocket. A precise hydrogen bond network in the center of the binding groove orients and positions the ceramide backbone for insertion of the lipid tails in their respective pockets. The 3'-sulfated galactose headgroup is highly exposed for presentation to the T cell receptor and projects up and away from the binding pocket due to its beta linkage, compared with the more intimate binding of the alpha-glactosyl ceramide headgroup to CD1d. These structure and binding data on sulfatide presentation by CD1d have important implications for the design of therapeutics that target T cells reactive for myelin glycolipids in autoimmune diseases of the central nervous system.

Structural basis for CD1d presentation of a sulfatide derived from myelin and its implications for autoimmunity.,Zajonc DM, Maricic I, Wu D, Halder R, Roy K, Wong CH, Kumar V, Wilson IA J Exp Med. 2005 Dec 5;202(11):1517-26. Epub 2005 Nov 28. PMID:16314439<ref>PMID:16314439</ref>

~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~

~~</div>~~

~~<div class="pdbe-citations 2akr" style="background-color:#fffaf0;"></div>~~

~~==See Also==~~

*[[Beta-2 microglobulin|Beta-2 microglobulin]]

*[[CD1|CD1]]

~~== References ==~~

~~<references/>~~

__TOC__

</StructureSection>

[[Category: ~~Lk3 transgenic mice~~]]

[[Category: Large Structures]]

[[Category: ~~Halder, R]]~~

[[Category: Z-disk]]

~~[[Category: Kumar, V]]~~

~~[[Category: Maricic, I]]~~

~~[[Category: Roy, K]]~~

~~[[Category: Wilson, I A]]~~

~~[[Category: Wong, C H]]~~

~~[[Category: Wu, D]]~~

~~[[Category: Zajonc, D M]]~~

~~[[Category: Cd1d]]~~

~~[[Category: Immune system]]~~

~~[[Category: Mhc fold]]~~

~~[[Category: Nkt cell]]~~

~~[[Category: Self~~-~~antigen]]~~

~~[[Category: Sulfatide]]~~

~~[[Category: Tcr~~]]

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@@ Line 1: / Line 1: @@
-==Structural basis of sulfatide presentation by mouse CD1d==
+====
-<StructureSection load='2akr' size='340' side='right' caption='[[2akr]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='2akr' size='340' side='right'caption='[[2akr]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2akr]] is a 4 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=2AKR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AKR FirstGlance]. <br>
+<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIS:(15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE'>CIS</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
+</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=2akr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2akr OCA], [https://pdbe.org/2akr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2akr RCSB], [https://www.ebi.ac.uk/pdbsum/2akr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2akr ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1cd1|1cd1]], [[1z5l|1z5l]], [[1zhn|1zhn]], [[1zt4|1zt4]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cd1d1, Cd1.1 ([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=2akr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2akr OCA], [http://pdbe.org/2akr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2akr RCSB], [http://www.ebi.ac.uk/pdbsum/2akr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2akr ProSAT]</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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 21: / Line 16: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2akr ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Sulfatide derived from the myelin stimulates a distinct population of CD1d-restricted natural killer T (NKT) cells. Cis-tetracosenoyl sulfatide is one of the immunodominant species in myelin as identified by proliferation, cytokine secretion, and CD1d tetramer staining. The crystal structure of mouse CD1d in complex with cis-tetracosenoyl sulfatide at 1.9 A resolution reveals that the longer cis-tetracosenoyl fatty acid chain fully occupies the A' pocket of the CD1d binding groove, whereas the sphingosine chain fills up the F' pocket. A precise hydrogen bond network in the center of the binding groove orients and positions the ceramide backbone for insertion of the lipid tails in their respective pockets. The 3'-sulfated galactose headgroup is highly exposed for presentation to the T cell receptor and projects up and away from the binding pocket due to its beta linkage, compared with the more intimate binding of the alpha-glactosyl ceramide headgroup to CD1d. These structure and binding data on sulfatide presentation by CD1d have important implications for the design of therapeutics that target T cells reactive for myelin glycolipids in autoimmune diseases of the central nervous system.
-Structural basis for CD1d presentation of a sulfatide derived from myelin and its implications for autoimmunity.,Zajonc DM, Maricic I, Wu D, Halder R, Roy K, Wong CH, Kumar V, Wilson IA J Exp Med. 2005 Dec 5;202(11):1517-26. Epub 2005 Nov 28. PMID:16314439<ref>PMID:16314439</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2akr" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Beta-2 microglobulin|Beta-2 microglobulin]]
-*[[CD1|CD1]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Lk3 transgenic mice]]
+[[Category: Large Structures]]
-[[Category: Halder, R]]
+[[Category: Z-disk]]
-[[Category: Kumar, V]]
-[[Category: Maricic, I]]
-[[Category: Roy, K]]
-[[Category: Wilson, I A]]
-[[Category: Wong, C H]]
-[[Category: Wu, D]]
-[[Category: Zajonc, D M]]
-[[Category: Cd1d]]
-[[Category: Immune system]]
-[[Category: Mhc fold]]
-[[Category: Nkt cell]]
-[[Category: Self-antigen]]
-[[Category: Sulfatide]]
-[[Category: Tcr]]