5oqf - Revision history

OCA at 16:58, 13 December 2023

OCA — Wed, 13 Dec 2023 16:58:09 GMT

←Older revision		Revision as of 16:58, 13 December 2023
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	<StructureSection load='5oqf' size='340' side='right'caption='[[5oqf]], [[Resolution\|resolution]] 2.27Å' scene=''>		<StructureSection load='5oqf' size='340' side='right'caption='[[5oqf]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oqf]] is a 2 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=5OQF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oqf]] is a 2 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=5OQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OQF FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">H2-K1, ~~H2-K (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=10090 LK3 transgenic mice])~~</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]] 2.27Å</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=5oqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oqf OCA], [~~http~~://pdbe.org/5oqf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5oqf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5oqf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5oqf 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=5oqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oqf OCA], [https://pdbe.org/5oqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oqf RCSB], [https://www.ebi.ac.uk/pdbsum/5oqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oqf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~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/HA1B_MOUSE HA1B_MOUSE] Involved in the presentation of foreign 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 ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Mikolajek, H]]	+	[[Category: Mikolajek H]]
-	[[Category: Werner~~, J M]]~~	+	[[Category: Werner JM]]
-	~~[[Category: Antigen]]~~	+
-	~~[[Category: Diagnosis]]~~	+
-	~~[[Category: Epitope]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Major histocompatibility complex]]~~	+
-	~~[[Category: Mice]]~~	+
-	~~[[Category: Model]]~~	+
-	~~[[Category: Molecular conformation]]~~	+
-	~~[[Category: Peptide]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: T-cell]]~~	+
-	~~[[Category: T-lymphocyte]]~~	+
-	~~[[Category: Vaccine~~]]	+

OCA at 06:57, 16 October 2019

OCA — Wed, 16 Oct 2019 06:57:25 GMT

←Older revision		Revision as of 06:57, 16 October 2019
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	==Crystal structure of a single chain trimer composed of the MHC 1 heavy chain H2-Kb WT, beta-2microglobulin, and ovalbumin derived peptide==		==Crystal structure of a single chain trimer composed of the MHC 1 heavy chain H2-Kb WT, beta-2microglobulin, and ovalbumin derived peptide==
-	<StructureSection load='5oqf' size='340' side='right' caption='[[5oqf]], [[Resolution\|resolution]] 2.27Å' scene=''>	+	<StructureSection load='5oqf' size='340' side='right'caption='[[5oqf]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5oqf]] is a 2 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=5OQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OQF FirstGlance]. <br>		<table><tr><td colspan='2'>[[5oqf]] is a 2 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=5OQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OQF FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Mikolajek, H]]		[[Category: Mikolajek, H]]

OCA at 06:29, 18 April 2018

OCA — Wed, 18 Apr 2018 06:29:21 GMT

←Older revision		Revision as of 06:29, 18 April 2018
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	<StructureSection load='5oqf' size='340' side='right' caption='[[5oqf]], [[Resolution\|resolution]] 2.27Å' scene=''>		<StructureSection load='5oqf' size='340' side='right' caption='[[5oqf]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oqf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oqf]] is a 2 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=5OQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OQF FirstGlance]. <br>
-	</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=5oqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oqf OCA], [http://pdbe.org/5oqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oqf RCSB], [http://www.ebi.ac.uk/pdbsum/5oqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oqf ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">H2-K1, H2-K ([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=5oqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oqf OCA], [http://pdbe.org/5oqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oqf RCSB], [http://www.ebi.ac.uk/pdbsum/5oqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oqf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Mikolajek, H]]		[[Category: Mikolajek, H]]
	[[Category: Werner, J M]]		[[Category: Werner, J M]]

OCA at 13:43, 11 April 2018

OCA — Wed, 11 Apr 2018 13:43:01 GMT

←Older revision		Revision as of 13:43, 11 April 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5oqf is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of a single chain trimer composed of the MHC 1 heavy chain H2-Kb WT, beta-2microglobulin, and ovalbumin derived peptide==
		+	<StructureSection load='5oqf' size='340' side='right' caption='[[5oqf]], [[Resolution\|resolution]] 2.27Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5oqf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OQF FirstGlance]. <br>
		+	</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=5oqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oqf OCA], [http://pdbe.org/5oqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oqf RCSB], [http://www.ebi.ac.uk/pdbsum/5oqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oqf ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[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 ==
		+	Endoplasmic reticulum aminopeptidase 1 (ERAP1) and ERAP2 process N-terminally extended antigenic precursors for optimal loading onto major histocompatibility complex class I (MHC I) molecules. We and others have demonstrated that ERAP1 processes peptides bound to MHC I, but the underlying mechanism is unknown. To this end, we utilized single-chain trimers (SCT) of the ovalbumin-derived epitope SIINFEKL (SL8) tethered to the H2-Kb MHC I determinant from mouse and introduced three substitutions, E63A, K66A, and W167A, at the A-pocket of the peptide-binding groove in the MHC I heavy chain, which interact with the N termini of peptides. These variants significantly decreased SL8-presenting SCT at the cell surface in the presence of ERAP1, but did not affect overall SCT expression, indicating that ERAP1 trims the SL8 N terminus. Comparison of the X-ray crystal structures of WT and three variant SCTs revealed only minor perturbations of the peptide-binding domain in the variants. However, molecular dynamics simulations suggested that SL8 can dissociate partially within a sub-microsecond timescale, exposing its N terminus to the solvent. We also found that the C terminus of MHC I-bound SL8 remains deeply buried in the F-pocket of MHC I. Furthermore, free-energy calculations revealed that the three SCT variants exhibit lower free-energy barriers of N terminus dissociation than the WT Kb. Taken together, our results are consistent with a previously observed model in which the partial dissociation of bound peptides from MHC I exposes their N terminus to trimming by ERAP1, while their C terminus is anchored at the F-pocket.

-	~~Authors~~:	+	The partial dissociation of MHC class I bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1.,Papakyriakou A, Reeves E, Beton M, Mikolajek H, Douglas L, Cooper G, Elliott T, Werner JM, James E J Biol Chem. 2018 Mar 29. pii: RA117.000313. doi: 10.1074/jbc.RA117.000313. PMID:29599287<ref>PMID:29599287</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5oqf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Mikolajek, H]]
		+	[[Category: Werner, J M]]
		+	[[Category: Antigen]]
		+	[[Category: Diagnosis]]
		+	[[Category: Epitope]]
		+	[[Category: Immune system]]
		+	[[Category: Major histocompatibility complex]]
		+	[[Category: Mice]]
		+	[[Category: Model]]
		+	[[Category: Molecular conformation]]
		+	[[Category: Peptide]]
		+	[[Category: Receptor]]
		+	[[Category: T-cell]]
		+	[[Category: T-lymphocyte]]
		+	[[Category: Vaccine]]

OCA at 05:42, 13 December 2017

OCA — Wed, 13 Dec 2017 05:42:45 GMT

←Older revision		Revision as of 05:42, 13 December 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5oqf is ON HOLD	+	The entry 5oqf is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5oqf" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:43:19 GMT

Protected "5oqf" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:43, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5oqf is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 12:43:18 GMT

New page: '''Unreleased structure''' The entry 5oqf is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5oqf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]