4l8d - Revision history

OCA at 16:14, 20 September 2023

2023-09-20T16:14:36Z

←Older revision		Revision as of 16:14, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4l8d]] is a 6 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=4L8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[4l8d]] is a 6 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=4L8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L8D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4l8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8d OCA], [https://pdbe.org/4l8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l8d RCSB], [https://www.ebi.ac.uk/pdbsum/4l8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8d 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=4l8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8d OCA], [https://pdbe.org/4l8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l8d RCSB], [https://www.ebi.ac.uk/pdbsum/4l8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8d ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:44, 14 December 2022

2022-12-14T10:44:12Z

←Older revision		Revision as of 10:44, 14 December 2022
Line 1:		Line 1:

	==Crystal structure of the H2Db in complex with the NP-N5D peptide==		==Crystal structure of the H2Db in complex with the NP-N5D peptide==
-	<StructureSection load='4l8d' size='340' side='right' caption='[[4l8d]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4l8d' size='340' side='right'caption='[[4l8d]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4l8d]] is a 6 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=4L8D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4L8D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4l8d]] is a 6 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=4L8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L8D 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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4huu\|4huu]], [[4huv\|4huv]], [[4huw\|4huw]], [[4hux\|4hux]], [[4hv8\|4hv8]], [[4l8b\|4l8b]], [[4l8c\|4l8c]]</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=4l8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8d OCA], [https://pdbe.org/4l8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l8d RCSB], [https://www.ebi.ac.uk/pdbsum/4l8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8d ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">H2-D1 ([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=4l8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8d OCA], [~~http~~://pdbe.org/4l8d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4l8d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4l8d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8d ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HA11_MOUSE HA11_MOUSE]] Involved in the presentation of foreign ~~antigens to the immune system. [[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/HA11_MOUSE HA11_MOUSE] Involved in the presentation of foreign antigens to the immune system.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 4l8d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4l8d" 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: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Gras, S~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Rossjohn, J~~]]	+	[[Category: Gras S]]
-	[[Category: ~~Immune system]]~~	+	[[Category: Rossjohn J]]
-	~~[[Category: Influenza]]~~	+
-	~~[[Category: T cell immunity]]~~	+
-	~~[[Category: Viral escape~~]]	+

OCA at 09:33, 15 November 2017

2017-11-15T09:33:37Z

←Older revision		Revision as of 09:33, 15 November 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4l8d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4l8d" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Beta-2 microglobulin\|Beta-2 microglobulin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:29, 5 August 2016

2016-08-05T20:29:53Z

←Older revision		Revision as of 20:29, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the H2Db in complex with the NP-N5D peptide==		==Crystal structure of the H2Db in complex with the NP-N5D peptide==
	<StructureSection load='4l8d' size='340' side='right' caption='[[4l8d]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4l8d' size='340' side='right' caption='[[4l8d]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4huu\|4huu]], [[4huv\|4huv]], [[4huw\|4huw]], [[4hux\|4hux]], [[4hv8\|4hv8]], [[4l8b\|4l8b]], [[4l8c\|4l8c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4huu\|4huu]], [[4huv\|4huv]], [[4huw\|4huw]], [[4hux\|4hux]], [[4hv8\|4hv8]], [[4l8b\|4l8b]], [[4l8c\|4l8c]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">H2-D1 ([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">H2-D1 ([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=4l8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4l8d RCSB], [http://www.ebi.ac.uk/pdbsum/4l8d 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=4l8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8d OCA], [http://pdbe.org/4l8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4l8d RCSB], [http://www.ebi.ac.uk/pdbsum/4l8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4l8d" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 21:39, 25 December 2014

2014-12-25T21:39:01Z

←Older revision		Revision as of 21:39, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4l8d\| PDB=4l8d \| SCENE= }}~~	+	==Crystal structure of the H2Db in complex with the NP-N5D peptide==
-	===Crystal structure of the H2Db in complex with the NP-N5D peptide===	+	<StructureSection load='4l8d' size='340' side='right' caption='[[4l8d]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24173108}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4l8d]] is a 6 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=4L8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4L8D FirstGlance]. <br>
-	==Function==	+	</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4huu\|4huu]], [[4huv\|4huv]], [[4huw\|4huw]], [[4hux\|4hux]], [[4hv8\|4hv8]], [[4l8b\|4l8b]], [[4l8c\|4l8c]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">H2-D1 ([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=4l8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4l8d RCSB], [http://www.ebi.ac.uk/pdbsum/4l8d PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/HA11_MOUSE HA11_MOUSE]] Involved in the presentation of foreign antigens to the immune system. [[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.		[[http://www.uniprot.org/uniprot/HA11_MOUSE HA11_MOUSE]] Involved in the presentation of foreign antigens to the immune system. [[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 ==
		+	Influenza A virus-specific CD8(+) cytotoxic T lymphocytes (CTLs) provide a degree of cross-strain protection that is potentially subverted by mutation. Here we describe the sequential emergence of such variants within CTL epitopes for a persistently infected, immunocompromised infant. Further analysis in immunodeficient and wild-type mice supports the view that CTL escape variants arise frequently in influenza, accumulate with time and revert in the absence of immune pressure under MHCI-mismatched conditions. Viral fitness, the abundance of endogenous CD8(+) T cell responses and T cell receptor repertoire diversity influence the nature of these de novo mutants. Structural characterization of dominant escape variants shows how the peptide-MHCI interaction is modified to affect variant-MHCI stability. The mechanism of influenza virus escape thus looks comparable to that recognized for chronic RNA viruses like HIV and HCV, suggesting that immunocompromised patients with prolonged viral infection could have an important part in the emergence of influenza quasispecies.
		+
		+	Acute emergence and reversion of influenza A virus quasispecies within CD8(+) T cell antigenic peptides.,Valkenburg SA, Quinones-Parra S, Gras S, Komadina N, McVernon J, Wang Z, Halim H, Iannello P, Cole C, Laurie K, Kelso A, Rossjohn J, Doherty PC, Turner SJ, Kedzierska K Nat Commun. 2013 Oct 30;4:2663. doi: 10.1038/ncomms3663. PMID:24173108<ref>PMID:24173108</ref>

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4l8d]] is~~ a ~~6 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=4L8D OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:024173108</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Beta-2 microglobulin\|Beta-2 microglobulin]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
-	[[Category: Gras, S.]]	+	[[Category: Gras, S]]
-	[[Category: Rossjohn, J.]]	+	[[Category: Rossjohn, J]]
	[[Category: Immune system]]		[[Category: Immune system]]
	[[Category: Influenza]]		[[Category: Influenza]]
	[[Category: T cell immunity]]		[[Category: T cell immunity]]
	[[Category: Viral escape]]		[[Category: Viral escape]]

OCA at 06:10, 4 December 2013

2013-12-04T06:10:44Z

←Older revision		Revision as of 06:10, 4 December 2013
Line 1:		Line 1:
	{{STRUCTURE_4l8d\| PDB=4l8d \| SCENE= }}		{{STRUCTURE_4l8d\| PDB=4l8d \| SCENE= }}
	===Crystal structure of the H2Db in complex with the NP-N5D peptide===		===Crystal structure of the H2Db in complex with the NP-N5D peptide===
		+	{{ABSTRACT_PUBMED_24173108}}

	==Function==		==Function==
Line 6:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4l8d]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8D OCA].	+	[[4l8d]] is a 6 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=4L8D OCA].
-	[[Category: ~~Mus musculus~~]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:024173108</ref><references group="xtra"/><references/>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Gras, S.]]		[[Category: Gras, S.]]
	[[Category: Rossjohn, J.]]		[[Category: Rossjohn, J.]]

OCA at 08:09, 16 October 2013

2013-10-16T08:09:08Z

←Older revision		Revision as of 08:09, 16 October 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4l8d\| PDB=4l8d \| SCENE= }}
		+	===Crystal structure of the H2Db in complex with the NP-N5D peptide===

-	~~The entry 4l8d is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/HA11_MOUSE HA11_MOUSE]] Involved in the presentation of foreign antigens to the immune system. [[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.

-	~~Authors~~: ~~Rossjohn, J~~., Gras, S.	+	==About this Structure==
-		+	[[4l8d]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8D OCA].
-	~~Description~~: ~~Crystal Structure of pMHC complex~~	+	[[Category: Mus musculus]]
		+	[[Category: Gras, S.]]
		+	[[Category: Rossjohn, J.]]
		+	[[Category: Immune system]]
		+	[[Category: Influenza]]
		+	[[Category: T cell immunity]]
		+	[[Category: Viral escape]]

OCA at 07:14, 14 August 2013

2013-08-14T07:14:49Z

←Older revision		Revision as of 07:14, 14 August 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4l8d is ON HOLD	+	The entry 4l8d is ON HOLD until Paper Publication

	Authors: Rossjohn, J., Gras, S.		Authors: Rossjohn, J., Gras, S.

	Description: Crystal Structure of pMHC complex		Description: Crystal Structure of pMHC complex

OCA at 12:25, 24 July 2013

2013-07-24T12:25:17Z

←Older revision		Revision as of 12:25, 24 July 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4l8d is ON HOLD ~~until sometime in the future~~	+	The entry 4l8d is ON HOLD

	Authors: Rossjohn, J., Gras, S.		Authors: Rossjohn, J., Gras, S.

	Description: Crystal Structure of pMHC complex		Description: Crystal Structure of pMHC complex

OCA at 15:06, 10 July 2013

2013-07-10T15:06:48Z

←Older revision		Revision as of 15:06, 10 July 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4l8d is ON HOLD	+	The entry 4l8d is ON HOLD until sometime in the future

	Authors: Rossjohn, J., Gras, S.		Authors: Rossjohn, J., Gras, S.

	Description: Crystal Structure of pMHC complex		Description: Crystal Structure of pMHC complex