OCA at 12:59, 1 February 2024

OCA — Thu, 01 Feb 2024 12:59:34 GMT

←Older revision		Revision as of 12:59, 1 February 2024
Line 1:		Line 1:

-	====	+	==CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV-DERIVED GP33 PEPTIDE with D-AMINOACID==
-	<StructureSection load='7p0t' size='340' side='right'caption='[[7p0t]]' scene=''>	+	<StructureSection load='7p0t' size='340' side='right'caption='[[7p0t]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7p0t]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lymphocytic_choriomeningitis_mammarenavirus Lymphocytic choriomeningitis mammarenavirus] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P0T FirstGlance]. <br>
-	</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=7p0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p0t OCA], [https://pdbe.org/7p0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p0t RCSB], [https://www.ebi.ac.uk/pdbsum/7p0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p0t ProSAT]</span></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]] 2.605Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DPN:D-PHENYLALANINE'>DPN</scene>, <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=7p0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p0t OCA], [https://pdbe.org/7p0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p0t RCSB], [https://www.ebi.ac.uk/pdbsum/7p0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p0t ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[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;">
		+	== Publication Abstract from PubMed ==
		+	Presentation of pathogen-derived epitopes by major histocompatibility complex I (MHC-I) can lead to the activation and expansion of specific CD8(+) T cell clones, eventually resulting in the destruction of infected target cells. Altered peptide ligands (APLs), designed to elicit immunogenicity toward a wild-type peptide, may affect the overall stability of MHC-I/peptide (pMHC) complexes and modulate the recognition by T cell receptors (TCR). Previous works have demonstrated that proline substitution at position 3 (p3P) of different MHC-restricted epitopes, including the immunodominant LCMV-derived epitope gp33 and escape variants, may be an effective design strategy to increase epitope immunogenicity. These studies hypothesized that the p3P substitution increases peptide rigidity, facilitating TCR binding. Here, molecular dynamics simulations indicate that the p3P modification rigidifies the APLs in solution predisposing them for the MHC-I loading as well as once bound to H-2D(b), predisposing them for TCR binding. Our results also indicate that peptide position 6, key for interaction of H-2D(b)/gp33 with the TCR P14, takes a suboptimal conformation before as well as after binding to the TCR. Analyses of H-2D(b) in complex with APLs, in which position 6 was subjected to an l- to d-amino acid modification, revealed small conformational changes and comparable pMHC thermal stability. However, the l- to d-modification reduced significantly the binding to P14 even in the presence of the p3P modification. Our combined data highlight the sensitivity of the TCR for the conformational dynamics of pMHC and provide further tools to dissect and modulate TCR binding and immunogenicity via APLs.
		+
		+	l- to d-Amino Acid Substitution in the Immunodominant LCMV-Derived Epitope gp33 Highlights the Sensitivity of the TCR Recognition Mechanism for the MHC/Peptide Structure and Dynamics.,Ballabio F, Broggini L, Paissoni C, Han X, Peqini K, Sala BM, Sun R, Sandalova T, Barbiroli A, Achour A, Pellegrino S, Ricagno S, Camilloni C ACS Omega. 2022 Mar 7;7(11):9622-9635. doi: 10.1021/acsomega.1c06964. eCollection , 2022 Mar 22. PMID:35350306<ref>PMID:35350306</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7p0t" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Lymphocytic choriomeningitis mammarenavirus]]
		+	[[Category: Mus musculus]]
		+	[[Category: Broggini L]]
		+	[[Category: Ricagno S]]

OCA at 11:18, 23 March 2022

OCA — Wed, 23 Mar 2022 11:18:04 GMT

←Older revision		Revision as of 11:18, 23 March 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7p0t ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7p0t' size='340' side='right'caption='[[7p0t]]' scene=''>
-	~~Authors~~: ~~Broggini, L~~.~~, Ricagno, S~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV~~-~~DERIVED GP33 PEPTIDE with D-AMINOACID~~	+	</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=7p0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p0t OCA], [https://pdbe.org/7p0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p0t RCSB], [https://www.ebi.ac.uk/pdbsum/7p0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p0t ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Ricagno, S~~]]	+	__TOC__
-	[[Category: ~~Broggini, L~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 09:27, 28 July 2021

OCA — Wed, 28 Jul 2021 09:27:53 GMT

←Older revision		Revision as of 09:27, 28 July 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7p0t is ON HOLD	+	The entry 7p0t is ON HOLD until Paper Publication

	Authors: Broggini, L., Ricagno, S.		Authors: Broggini, L., Ricagno, S.

OCA: Protected "7p0t" [edit=sysop:move=sysop]

OCA — Wed, 07 Jul 2021 08:54:49 GMT

Protected "7p0t" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:54, 7 July 2021

OCA: New page: '''Unreleased structure''' The entry 7p0t is ON HOLD Authors: Broggini, L., Ricagno, S. Description: CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN C...

OCA — Wed, 07 Jul 2021 08:54:48 GMT

New page: '''Unreleased structure''' The entry 7p0t is ON HOLD Authors: Broggini, L., Ricagno, S. Description: CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN C...

New page

'''Unreleased structure'''

The entry 7p0t is ON HOLD

Authors: Broggini, L., Ricagno, S.

Description: CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV-DERIVED GP33 PEPTIDE with D-AMINOACID
[[Category: Unreleased Structures]]
[[Category: Ricagno, S]]
[[Category: Broggini, L]]

7p0t - Revision history

OCA at 12:59, 1 February 2024

OCA at 11:18, 23 March 2022

OCA at 09:27, 28 July 2021

OCA: Protected "7p0t" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7p0t is ON HOLD Authors: Broggini, L., Ricagno, S. Description: CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN C...