3tyf - Revision history

OCA at 05:50, 13 July 2022

OCA — Wed, 13 Jul 2022 05:50:26 GMT

←Older revision		Revision as of 05:50, 13 July 2022
Line 1:		Line 1:

	==Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR==		==Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR==
-	<StructureSection load='3tyf' size='340' side='right' caption='[[3tyf]], [[Resolution\|resolution]] 2.81Å' scene=''>	+	<StructureSection load='3tyf' size='340' side='right'caption='[[3tyf]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tyf]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TYF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tyf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TYF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tzv\|3tzv]], [[3u0p\|3u0p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3tzv\|3tzv]], [[3u0p\|3u0p]]</div></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=3tyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tyf OCA], [~~http~~://pdbe.org/3tyf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3tyf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3tyf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3tyf 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=3tyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tyf OCA], [https://pdbe.org/3tyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tyf RCSB], [https://www.ebi.ac.uk/pdbsum/3tyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tyf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Adams, E J]]		[[Category: Adams, E J]]
	[[Category: Lopez-Sagaseta, J]]		[[Category: Lopez-Sagaseta, J]]

OCA at 10:58, 11 August 2016

OCA — Thu, 11 Aug 2016 10:58:59 GMT

←Older revision		Revision as of 10:58, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR==		==Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR==
	<StructureSection load='3tyf' size='340' side='right' caption='[[3tyf]], [[Resolution\|resolution]] 2.81Å' scene=''>		<StructureSection load='3tyf' size='340' side='right' caption='[[3tyf]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tyf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tyf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TYF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tzv\|3tzv]], [[3u0p\|3u0p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tzv\|3tzv]], [[3u0p\|3u0p]]</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=3tyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tyf RCSB], [http://www.ebi.ac.uk/pdbsum/3tyf PDBsum]</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=3tyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tyf OCA], [http://pdbe.org/3tyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tyf RCSB], [http://www.ebi.ac.uk/pdbsum/3tyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tyf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3tyf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Adams, E J]]		[[Category: Adams, E J]]
	[[Category: Lopez-Sagaseta, J]]		[[Category: Lopez-Sagaseta, J]]

OCA at 09:30, 4 January 2015

OCA — Sun, 04 Jan 2015 09:30:48 GMT

←Older revision		Revision as of 09:30, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3tyf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TYF FirstGlance]. <br>		<table><tr><td colspan='2'>[[3tyf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TYF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tzv\|3tzv]], [[3u0p\|3u0p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tzv\|3tzv]], [[3u0p\|3u0p]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3tyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tyf RCSB], [http://www.ebi.ac.uk/pdbsum/3tyf PDBsum]</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=3tyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tyf RCSB], [http://www.ebi.ac.uk/pdbsum/3tyf PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 13:		Line 13:
	Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor.,Lopez-Sagaseta J, Sibener LV, Kung JE, Gumperz J, Adams EJ EMBO J. 2012 Mar 6;31(8):2047-59. doi: 10.1038/emboj.2012.54. PMID:22395072<ref>PMID:22395072</ref>		Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor.,Lopez-Sagaseta J, Sibener LV, Kung JE, Gumperz J, Adams EJ EMBO J. 2012 Mar 6;31(8):2047-59. doi: 10.1038/emboj.2012.54. PMID:22395072<ref>PMID:22395072</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 20:		Line 20:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Adams, E J.]]	+	[[Category: Adams, E J]]
-	[[Category: Lopez-Sagaseta, J.]]	+	[[Category: Lopez-Sagaseta, J]]
	[[Category: Antigen recognition]]		[[Category: Antigen recognition]]
	[[Category: Cd1d]]		[[Category: Cd1d]]

OCA at 06:05, 5 June 2014

OCA — Thu, 05 Jun 2014 06:05:57 GMT

←Older revision		Revision as of 06:05, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3tyf.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR==
		+	<StructureSection load='3tyf' size='340' side='right' caption='[[3tyf]], [[Resolution\|resolution]] 2.81Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3tyf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TYF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tzv\|3tzv]], [[3u0p\|3u0p]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3tyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tyf RCSB], [http://www.ebi.ac.uk/pdbsum/3tyf PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Invariant Natural Killer T (iNKT) cells use highly restricted alphabeta T cell receptors (TCRs) to probe the repertoire of lipids presented by CD1d molecules. Here, we describe our studies of lysophosphatidylcholine (LPC) presentation by human CD1d and its recognition by a native, LPC-specific iNKT TCR. Human CD1d presenting LPC adopts an altered conformation from that of CD1d presenting glycolipid antigens, with a shifted alpha1 helix resulting in an open A' pocket. Binding of the iNKT TCR requires a 7-A displacement of the LPC headgroup but stabilizes the CD1d-LPC complex in a closed conformation. The iNKT TCR CDR loop footprint on CD1d-LPC is anchored by the conserved positioning of the CDR3alpha loop, whereas the remaining CDR loops are shifted, due in part to amino-acid differences in the CDR3beta and Jbeta segment used by this iNKT TCR. These findings provide insight into how lysophospholipids are presented by human CD1d molecules and how this complex is recognized by some, but not all, human iNKT cells.

-	<!--	+	Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor.,Lopez-Sagaseta J, Sibener LV, Kung JE, Gumperz J, Adams EJ EMBO J. 2012 Mar 6;31(8):2047-59. doi: 10.1038/emboj.2012.54. PMID:22395072<ref>PMID:22395072</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3tyf"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_3tyf\| PDB=3tyf \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~a CD1d-lysophosphatidylcholine reactive iNKT TCR===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22395072}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22395072 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22395072}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3tyf]] is a 4 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TYF OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022395072<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Adams, E J.]]		[[Category: Adams, E J.]]

OCA at 09:16, 25 April 2012

OCA — Wed, 25 Apr 2012 09:16:41 GMT

←Older revision		Revision as of 09:16, 25 April 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3tyf.jpg\|left\|200px]]

-	The ~~entry 3tyf~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3tyf", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3tyf\| PDB=3tyf \| SCENE= }}

-	~~Authors: Lopez~~-~~Sagaseta, J., Adams, E.J.~~	+	===Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR===

-	~~Description~~: ~~Crystal structure of~~ a ~~CD1d~~-~~lysophosphatidylcholine reactive iNKT TCR~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22395072}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22395072 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22395072}}
		+
		+	==About this Structure==
		+	[[3tyf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TYF OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022395072</ref><references group="xtra"/>
		+	[[Category: Escherichia coli]]
		+	[[Category: Adams, E J.]]
		+	[[Category: Lopez-Sagaseta, J.]]
		+	[[Category: Antigen recognition]]
		+	[[Category: Cd1d]]
		+	[[Category: Immune system]]
		+	[[Category: Immunoglobulin-like]]
		+	[[Category: Membrane]]

OCA at 06:01, 14 March 2012

OCA — Wed, 14 Mar 2012 06:01:13 GMT

←Older revision		Revision as of 06:01, 14 March 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3tyf is ON HOLD	+	The entry 3tyf is ON HOLD until Paper Publication

	Authors: Lopez-Sagaseta, J., Adams, E.J.		Authors: Lopez-Sagaseta, J., Adams, E.J.

	Description: Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR		Description: Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR

OCA at 08:46, 30 October 2011

OCA — Sun, 30 Oct 2011 08:46:10 GMT

←Older revision		Revision as of 08:46, 30 October 2011
Line 3:		Line 3:
	The entry 3tyf is ON HOLD		The entry 3tyf is ON HOLD

-	Authors: ~~L pez~~-Sagaseta, J, Adams, EJ	+	Authors: Lopez-Sagaseta, J., Adams, E.J.

	Description: Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR		Description: Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR

OCA: Protected "3tyf" [edit=sysop:move=sysop]

OCA — Wed, 05 Oct 2011 06:13:17 GMT

Protected "3tyf" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:13, 5 October 2011

OCA: New page: '''Unreleased structure''' The entry 3tyf is ON HOLD Authors: L pez-Sagaseta, J, Adams, EJ Description: Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR

OCA — Wed, 05 Oct 2011 06:13:15 GMT

New page: '''Unreleased structure''' The entry 3tyf is ON HOLD Authors: L pez-Sagaseta, J, Adams, EJ Description: Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR

New page

'''Unreleased structure'''

The entry 3tyf is ON HOLD

Authors: L pez-Sagaseta, J, Adams, EJ

Description: Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR