6bmk - Revision history

OCA at 14:45, 4 October 2023

OCA — Wed, 04 Oct 2023 14:45:45 GMT

←Older revision		Revision as of 14:45, 4 October 2023
Line 1:		Line 1:

	==Crystal structure of MHC-I like protein==		==Crystal structure of MHC-I like protein==
-	<StructureSection load='6bmk' size='340' side='right' caption='[[6bmk]], [[Resolution\|resolution]] 2.43Å' scene=''>	+	<StructureSection load='6bmk' size='340' side='right'caption='[[6bmk]], [[Resolution\|resolution]] 2.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bmk]] 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=6BMK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BMK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bmk]] is a 4 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=6BMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BMK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F57:(2R)-1-(decanoyloxy)-3-(phosphonooxy)propan-2-yl+octadecanoate'>F57</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.43Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cd1d2, Cd1.2 ([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=F57:(2R)-1-(decanoyloxy)-3-(phosphonooxy)propan-2-yl+octadecanoate'>F57</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6bmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmk OCA], [~~http~~://pdbe.org/6bmk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bmk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bmk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmk 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=6bmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmk OCA], [https://pdbe.org/6bmk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bmk RCSB], [https://www.ebi.ac.uk/pdbsum/6bmk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http://www.uniprot.org/uniprot/CD1D2_MOUSE CD1D2_MOUSE]] Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells. [[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/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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6bmk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6bmk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
		+	*[[CD1\|CD1]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Khandokar, Y B~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Nours, J Le~~]]	+	[[Category: Khandokar YB]]
-	[[Category: ~~Rossjohn,~~ J]]	+	[[Category: Le Nours J]]
-	[[Category: ~~Antigen]]~~	+	[[Category: Rossjohn J]]
-	~~[[Category: Cd1d]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Major histocompatibility complex]]~~	+
-	~~[[Category: Mhc-i~~]]	+

OCA at 06:20, 8 March 2018

OCA — Thu, 08 Mar 2018 06:20:51 GMT

←Older revision		Revision as of 06:20, 8 March 2018
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bmk]] 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=6BMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BMK FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bmk]] 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=6BMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BMK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MX7~~:(2R)-3-(~~PHOSPHONOOXY~~)~~PROPANE~~-~~1,2~~-~~DIYL+~~(~~9Z,9Z~~)~~BIS~~-~~OCTADEC~~-~~9-ENOATE~~'>~~MX7~~</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F57:(2R)-1-(decanoyloxy)-3-(phosphonooxy)propan-2-yl+octadecanoate'>F57</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cd1d2, Cd1.2 ([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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cd1d2, Cd1.2 ([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=6bmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmk OCA], [http://pdbe.org/6bmk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bmk RCSB], [http://www.ebi.ac.uk/pdbsum/6bmk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmk 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=6bmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmk OCA], [http://pdbe.org/6bmk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bmk RCSB], [http://www.ebi.ac.uk/pdbsum/6bmk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmk ProSAT]</span></td></tr>

OCA at 08:27, 22 February 2018

OCA — Thu, 22 Feb 2018 08:27:37 GMT

←Older revision		Revision as of 08:27, 22 February 2018
Line 3:		Line 3:
	<StructureSection load='6bmk' size='340' side='right' caption='[[6bmk]], [[Resolution\|resolution]] 2.43Å' scene=''>		<StructureSection load='6bmk' size='340' side='right' caption='[[6bmk]], [[Resolution\|resolution]] 2.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bmk]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BMK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bmk]] 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=6BMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BMK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MX7:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+(9Z,9Z)BIS-OCTADEC-9-ENOATE'>MX7</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MX7:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+(9Z,9Z)BIS-OCTADEC-9-ENOATE'>MX7</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cd1d2, Cd1.2 ([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=6bmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmk OCA], [http://pdbe.org/6bmk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bmk RCSB], [http://www.ebi.ac.uk/pdbsum/6bmk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmk 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=6bmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmk OCA], [http://pdbe.org/6bmk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bmk RCSB], [http://www.ebi.ac.uk/pdbsum/6bmk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmk ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Khandokar, Y B]]		[[Category: Khandokar, Y B]]
	[[Category: Nours, J Le]]		[[Category: Nours, J Le]]

OCA at 05:58, 31 January 2018

OCA — Wed, 31 Jan 2018 05:58:03 GMT

←Older revision		Revision as of 05:58, 31 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6bmk is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of MHC-I like protein==
		+	<StructureSection load='6bmk' size='340' side='right' caption='[[6bmk]], [[Resolution\|resolution]] 2.43Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6bmk]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BMK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MX7:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+(9Z,9Z)BIS-OCTADEC-9-ENOATE'>MX7</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6bmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmk OCA], [http://pdbe.org/6bmk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bmk RCSB], [http://www.ebi.ac.uk/pdbsum/6bmk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CD1D2_MOUSE CD1D2_MOUSE]] Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells. [[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 ==
		+	MHC class I-like CD1 molecules have evolved to present lipid-based antigens to T cells. Differences in the antigen-binding clefts of the CD1 family members determine the conformation and size of the lipids that are presented, although the factors that shape CD1 diversity remain unclear. In mice, two homologous genes, CD1D1 and CD1D2, encode the CD1d protein, which is essential to the development and function of natural killer T (NKT) cells. However, it remains unclear whether both CD1d isoforms are equivalent in their antigen presentation capacity and functions. Here, we report that CD1d2 molecules are expressed in the thymus of some mouse strains, where they select functional type I NKT cells. Intriguingly, the T cell antigen receptor repertoire and phenotype of CD1d2-selected type I NKT cells in CD1D1(-/-) mice differed from CD1d1-selected type I NKT cells. The structures of CD1d2 in complex with endogenous lipids and a truncated acyl-chain analog of alpha-galactosylceramide revealed that its A'-pocket was restricted in size compared with CD1d1. Accordingly, CD1d2 molecules could not present glycolipid antigens with long acyl chains efficiently, favoring the presentation of short acyl chain antigens. These results indicate that the two CD1d molecules present different sets of self-antigen(s) in the mouse thymus, thereby impacting the development of invariant NKT cells.

-	~~Authors: Khandokar~~, Y~~.B.~~, Le Nours, J., ~~Rossjohn~~, J.	+	Differing roles of CD1d2 and CD1d1 proteins in type I natural killer T cell development and function.,Sundararaj S, Zhang J, Krovi SH, Bedel R, Tuttle KD, Veerapen N, Besra GS, Khandokar Y, Praveena T, Le Nours J, Matsuda JL, Rossjohn J, Gapin L Proc Natl Acad Sci U S A. 2018 Jan 19. pii: 1716669115. doi:, 10.1073/pnas.1716669115. PMID:29351991<ref>PMID:29351991</ref>

-	~~Description: Crystal structure~~ of ~~MHC-I like protein~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Le Nours~~, J]]	+	<div class="pdbe-citations 6bmk" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Khandokar~~, ~~Y.B~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Khandokar, Y B]]
		+	[[Category: Nours, J Le]]
	[[Category: Rossjohn, J]]		[[Category: Rossjohn, J]]
		+	[[Category: Antigen]]
		+	[[Category: Cd1d]]
		+	[[Category: Immune system]]
		+	[[Category: Major histocompatibility complex]]
		+	[[Category: Mhc-i]]

OCA at 04:58, 20 December 2017

OCA — Wed, 20 Dec 2017 04:58:09 GMT

←Older revision		Revision as of 04:58, 20 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Khandokar, Y.B., Le Nours, J., Rossjohn, J.		Authors: Khandokar, Y.B., Le Nours, J., Rossjohn, J.

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

OCA — Wed, 22 Nov 2017 06:36:53 GMT

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

←Older revision

Revision as of 06:36, 22 November 2017

OCA: New page: '''Unreleased structure''' The entry 6bmk is ON HOLD Authors: Khandokar, Y.B., Le Nours, J., Rossjohn, J. Description: Crystal structure of MHC-I like protein [[Category: Unreleased St...

OCA — Wed, 22 Nov 2017 06:36:52 GMT

New page: '''Unreleased structure''' The entry 6bmk is ON HOLD Authors: Khandokar, Y.B., Le Nours, J., Rossjohn, J. Description: Crystal structure of MHC-I like protein [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 6bmk is ON HOLD

Authors: Khandokar, Y.B., Le Nours, J., Rossjohn, J.

Description: Crystal structure of MHC-I like protein
[[Category: Unreleased Structures]]
[[Category: Le Nours, J]]
[[Category: Khandokar, Y.B]]
[[Category: Rossjohn, J]]