4l8s - Revision history

OCA at 10:44, 14 December 2022

OCA — Wed, 14 Dec 2022 10:44:45 GMT

←Older revision		Revision as of 10:44, 14 December 2022
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	==Crystal structure of a human Valpha7.2/Vbeta13.3 MAIT TCR in complex with bovine MR1==		==Crystal structure of a human Valpha7.2/Vbeta13.3 MAIT TCR in complex with bovine MR1==
-	<StructureSection load='4l8s' size='340' side='right' caption='[[4l8s]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='4l8s' size='340' side='right'caption='[[4l8s]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4l8s]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bovin Bovin~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4L8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4l8s]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L8S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><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" id="ligandDat"><scene name='pdbligand=KFP:N~6~-[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]-D-LYSINE'>KFP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr~~ id~~='NonStdRes'><td class~~="~~sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat~~"><scene name='pdbligand=KFP:N~6~-[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]-D-LYSINE'>KFP</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=4l8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8s OCA], [https://pdbe.org/4l8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l8s RCSB], [https://www.ebi.ac.uk/pdbsum/4l8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8s ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[4iiq\|4iiq]], [[4l9l\|4l9l]]</td></tr>~~	+
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">MR1, Bt.63045 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])~~</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=4l8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8s OCA], [~~http~~://pdbe.org/4l8s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4l8s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4l8s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8s ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q6P4G7_HUMAN Q6P4G7_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4l8s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4l8s" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
		+	*[[T-cell receptor 3D structures\|T-cell receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bovin~~]]	+	[[Category: Bos taurus]]
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Adams, E J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Lopez-Sagaseta, J~~]]	+	[[Category: Adams EJ]]
-	[[Category: ~~Antigen]]~~	+	[[Category: Lopez-Sagaseta J]]
-	~~[[Category: Antigen presentation]]~~	+
-	~~[[Category: Antigen recognition]]~~	+
-	~~[[Category: Cell membrane]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immunoglobulin domain]]~~	+
-	~~[[Category: Mhc~~-~~class i~~]]	+

OCA at 22:31, 15 November 2017

OCA — Wed, 15 Nov 2017 22:31:22 GMT

←Older revision		Revision as of 22:31, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='4l8s' size='340' side='right' caption='[[4l8s]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='4l8s' size='340' side='right' caption='[[4l8s]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4l8s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4L8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4l8s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4L8S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KFP:N~6~-[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]-D-LYSINE'>KFP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KFP:N~6~-[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]-D-LYSINE'>KFP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iiq\|4iiq]], [[4l9l\|4l9l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iiq\|4iiq]], [[4l9l\|4l9l]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MR1, Bt.63045 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])</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=4l8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8s OCA], [http://pdbe.org/4l8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4l8s RCSB], [http://www.ebi.ac.uk/pdbsum/4l8s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8s 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=4l8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8s OCA], [http://pdbe.org/4l8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4l8s RCSB], [http://www.ebi.ac.uk/pdbsum/4l8s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8s ProSAT]</span></td></tr>
	</table>		</table>
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4l8s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4l8s" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Beta-2 microglobulin\|Beta-2 microglobulin]]
-	*[[T-cell receptor\|T-cell receptor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bovin]]
	[[Category: Human]]		[[Category: Human]]
	[[Category: Adams, E J]]		[[Category: Adams, E J]]

OCA at 13:04, 11 August 2016

OCA — Thu, 11 Aug 2016 13:04:13 GMT

←Older revision		Revision as of 13:04, 11 August 2016
Line 1:		Line 1:
-	{{STRUCTURE_4l8s\| PDB=4l8s \| SCENE= }}
-	===Crystal structure of a human Valpha7.2/Vbeta13.3 MAIT TCR in complex with bovine MR1===
-	{{ABSTRACT_PUBMED_24108697}}

-	==~~About this Structure~~==	+	==Crystal structure of a human Valpha7.2/Vbeta13.3 MAIT TCR in complex with bovine MR1==
-	[[4l8s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/ ~~], [http://en.wikipedia.org/wiki/Bovin Bovin~~] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8S OCA].	+	<StructureSection load='4l8s' size='340' side='right' caption='[[4l8s]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4l8s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4L8S FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KFP:N~6~-[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]-D-LYSINE'>KFP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iiq\|4iiq]], [[4l9l\|4l9l]]</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=4l8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8s OCA], [http://pdbe.org/4l8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4l8s RCSB], [http://www.ebi.ac.uk/pdbsum/4l8s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8s ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	MR1-restricted mucosal-associated invariant T (MAIT) cells represent a subpopulation of alphabeta T cells with innate-like properties and limited TCR diversity. MAIT cells are of interest because of their reactivity against bacterial and yeast species, suggesting that they play a role in defense against pathogenic microbes. Despite the advances in understanding MAIT cell biology, the molecular and structural basis behind their ability to detect MR1-Ag complexes is unclear. In this study, we present our structural and biochemical characterization of MAIT TCR engagement of MR1 presenting an Escherichia coli-derived stimulatory ligand, rRL-6-CH2OH, previously found in Salmonella typhimurium. We show a clear enhancement of MAIT TCR binding to MR1 due to the presentation of this ligand. Our structure of a MAIT TCR/MR1/rRL-6-CH2OH complex shows an evolutionarily conserved binding orientation, with a clear role for both the CDR3alpha and CDR3beta loops in recognizing the rRL-6-CH2OH stimulatory ligand. We also present two additional xenoreactive MAIT TCR/MR1 complexes that recapitulate the docking orientation documented previously, despite having variation in the CDR2beta and CDR3beta loop sequences. Our data support a model by which MAIT TCRs engage MR1 in a conserved fashion, with their binding affinities modulated by the nature of the MR1-presented Ag or diversity introduced by alternate Vbeta usage or CDR3beta sequences.

-	~~==Reference==~~	+	MAIT Recognition of a Stimulatory Bacterial Antigen Bound to MR1.,Lopez-Sagaseta J, Dulberger CL, McFedries A, Cushman M, Saghatelian A, Adams EJ J Immunol. 2013 Nov 15;191(10):5268-77. doi: 10.4049/jimmunol.1301958. Epub 2013 , Oct 9. PMID:24108697<ref>PMID:24108697</ref>
-	<ref ~~group="xtra"~~>PMID:~~024108697~~</ref><~~references group~~="~~xtra~~"/><~~references~~/>	+
-	[[~~Category: Bovin~~]]	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4l8s" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin\|Beta-2 microglobulin]]
		+	*[[T-cell receptor\|T-cell receptor]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Human]]		[[Category: Human]]
-	[[Category: Adams, E J.]]	+	[[Category: Adams, E J]]
-	[[Category: Lopez-Sagaseta, J.]]	+	[[Category: Lopez-Sagaseta, J]]
	[[Category: Antigen]]		[[Category: Antigen]]
	[[Category: Antigen presentation]]		[[Category: Antigen presentation]]

OCA at 12:05, 20 November 2013

OCA — Wed, 20 Nov 2013 12:05:04 GMT

←Older revision		Revision as of 12:05, 20 November 2013
Line 1:		Line 1:
	{{STRUCTURE_4l8s\| PDB=4l8s \| SCENE= }}		{{STRUCTURE_4l8s\| PDB=4l8s \| SCENE= }}
	===Crystal structure of a human Valpha7.2/Vbeta13.3 MAIT TCR in complex with bovine MR1===		===Crystal structure of a human Valpha7.2/Vbeta13.3 MAIT TCR in complex with bovine MR1===
		+	{{ABSTRACT_PUBMED_24108697}}

	==About this Structure==		==About this Structure==
-	[[4l8s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bos_taurus Bos taurus~~] and [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8S OCA].	+	[[4l8s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Bovin Bovin] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8S OCA].
-	[[Category: ~~Bos taurus~~]]	+
-	[[Category: ~~Homo sapiens~~]]	+	==Reference==
		+	<ref group="xtra">PMID:024108697</ref><references group="xtra"/><references/>
		+	[[Category: Bovin]]
		+	[[Category: Human]]
	[[Category: Adams, E J.]]		[[Category: Adams, E J.]]
	[[Category: Lopez-Sagaseta, J.]]		[[Category: Lopez-Sagaseta, J.]]

OCA at 08:09, 16 October 2013

OCA — Wed, 16 Oct 2013 08:09:14 GMT

←Older revision		Revision as of 08:09, 16 October 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4l8s\| PDB=4l8s \| SCENE= }}
		+	===Crystal structure of a human Valpha7.2/Vbeta13.3 MAIT TCR in complex with bovine MR1===

-	~~The entry~~ 4l8s is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4l8s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8S OCA].
-	~~Authors~~: Lopez-Sagaseta, J.~~, Adams, E.J.~~	+	[[Category: Bos taurus]]
-		+	[[Category: Homo sapiens]]
-	~~Description~~:	+	[[Category: Adams, E J.]]
		+	[[Category: Lopez-Sagaseta, J.]]
		+	[[Category: Antigen]]
		+	[[Category: Antigen presentation]]
		+	[[Category: Antigen recognition]]
		+	[[Category: Cell membrane]]
		+	[[Category: Immune system]]
		+	[[Category: Immunoglobulin domain]]
		+	[[Category: Mhc-class i]]

OCA at 04:41, 12 September 2013

OCA — Thu, 12 Sep 2013 04:41:25 GMT

←Older revision		Revision as of 04:41, 12 September 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4l8s is ON HOLD	+	The entry 4l8s is ON HOLD until Paper Publication

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

	Description:		Description:

OCA: Protected "4l8s" [edit=sysop:move=sysop]

OCA — Sun, 30 Jun 2013 09:03:33 GMT

Protected "4l8s" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:03, 30 June 2013

OCA: New page: '''Unreleased structure''' The entry 4l8s is ON HOLD Authors: Lopez-Sagaseta, J., Adams, E.J. Description:

OCA — Sun, 30 Jun 2013 09:03:32 GMT

New page: '''Unreleased structure''' The entry 4l8s is ON HOLD Authors: Lopez-Sagaseta, J., Adams, E.J. Description:

New page

'''Unreleased structure'''

The entry 4l8s is ON HOLD

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

Description: