7byd - Revision history

OCA at 15:41, 29 November 2023

2023-11-29T15:41:06Z

←Older revision		Revision as of 15:41, 29 November 2023
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-	====	+	==Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104==
-	<StructureSection load='7byd' size='340' side='right'caption='[[7byd]]' scene=''>	+	<StructureSection load='7byd' size='340' side='right'caption='[[7byd]], [[Resolution\|resolution]] 2.80Å' 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'>[[7byd]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Macaca_mulatta Macaca mulatta] and [https://en.wikipedia.org/wiki/Simian_immunodeficiency_virus Simian immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BYD 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=7byd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byd OCA], [https://pdbe.org/7byd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7byd RCSB], [https://www.ebi.ac.uk/pdbsum/7byd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7byd 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]] 2.8000326Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=7byd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byd OCA], [https://pdbe.org/7byd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7byd RCSB], [https://www.ebi.ac.uk/pdbsum/7byd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7byd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B2ZHY7_MACMU B2ZHY7_MACMU]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The covalent conjugation of a 14-carbon fatty acid (myristic acid) to the N-terminal Gly residue, termed N-myristoylation, occurs in some viral proteins to dictate their pathological function. This protein lipidation reaction, however, is monitored by host cytotoxic T lymphocytes that are capable of recognizing N-terminal lipopeptide fragments in the context of major histocompatibility complex (MHC) class I molecules. In a rhesus model of human AIDS, for example, the classical MHC class I allomorph, Mamu-B05104, was shown to bind SIV Nef-derived 4-mer lipopeptides (myristic acid-Gly-Gly-Ala-Ile; C14nef4) and present them to the CD8+ T-cell line, SN45. These lipopeptides accommodated in MHC class I molecules expose much shorter peptide chains than conventional MHC class I-presented 8-10-mer peptides, and the molecular mechanisms by which alphabeta T-cell receptors (TCRs) recognize lipopeptides currently remain unclear. An X-ray crystallographic analysis of the SN45 TCR alpha and beta heterodimer in a form that was co-crystallized with the C14nef4-bound Mamu-B05104 complex indicated that the amide group of the N-myristoylated glycine residue offered a primary T-cell epitope by establishing a sole hydrogen bond between its nitrogen atom and the side chain of Glu at position 101 of CDR3beta. Accordingly, the Glu to Ala mutation at this position resulted in the loss of lipopeptide recognition. On the other hand, TCRs were positioned remotely from the peptide portion of C14nef4, and strong interactions were not observed. Thus, these observations provide novel structural insights into lipopeptide recognition by TCRs, which contrast sharply with the general molecular principle of peptide recognition.
		+
		+	Crystal structure of the ternary complex of TCR, MHC class I and lipopeptides.,Morita D, Iwashita C, Mizutani T, Mori N, Mikami B, Sugita M Int Immunol. 2020 Nov 23;32(12):805-810. doi: 10.1093/intimm/dxaa050. PMID:32720986<ref>PMID:32720986</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7byd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
		+	*[[MHC 3D structures\|MHC 3D structures]]
		+	*[[MHC I 3D structures\|MHC I 3D structures]]
		+	*[[T-cell receptor 3D structures\|T-cell receptor 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Macaca mulatta]]
		+	[[Category: Simian immunodeficiency virus]]
		+	[[Category: Iwashita C]]
		+	[[Category: Morita D]]
		+	[[Category: Sugita M]]

OCA at 10:31, 31 March 2021

2021-03-31T10:31:35Z

←Older revision		Revision as of 10:31, 31 March 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7byd ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7byd' size='340' side='right'caption='[[7byd]]' scene=''>
-	~~Authors~~: ~~Morita, D~~.~~, Sugita, M~~.~~, Iwashita, C~~.	+	== 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 SN45 TCR in complex with lipopeptide-bound Mamu~~-~~B*05104~~	+	</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=7byd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byd OCA], [https://pdbe.org/7byd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7byd RCSB], [https://www.ebi.ac.uk/pdbsum/7byd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7byd ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Iwashita~~, C]]	+	__TOC__
-	[[Category: ~~Morita, D~~]]	+	</StructureSection>
-	[[Category: ~~Sugita, M~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 08:22, 22 July 2020

2020-07-22T08:22:41Z

←Older revision		Revision as of 08:22, 22 July 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Morita, D., Sugita, M., Iwashita, C.		Authors: Morita, D., Sugita, M., Iwashita, C.

OCA at 11:21, 8 July 2020

2020-07-08T11:21:41Z

←Older revision		Revision as of 11:21, 8 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7byd is ON HOLD ~~until Paper Publication~~	+	The entry 7byd is ON HOLD

	Authors: Morita, D., Sugita, M., Iwashita, C.		Authors: Morita, D., Sugita, M., Iwashita, C.

OCA at 04:52, 6 May 2020

2020-05-06T04:52:45Z

←Older revision		Revision as of 04:52, 6 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Morita, D., Sugita, M., Iwashita, C.		Authors: Morita, D., Sugita, M., Iwashita, C.

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

2020-04-29T05:38:13Z

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

←Older revision

Revision as of 05:38, 29 April 2020

OCA: New page: '''Unreleased structure''' The entry 7byd is ON HOLD Authors: Morita, D., Sugita, M., Iwashita, C. Description: Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*0...

2020-04-29T05:38:11Z

New page: '''Unreleased structure''' The entry 7byd is ON HOLD Authors: Morita, D., Sugita, M., Iwashita, C. Description: Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*0...

New page

'''Unreleased structure'''

The entry 7byd is ON HOLD

Authors: Morita, D., Sugita, M., Iwashita, C.

Description: Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104
[[Category: Unreleased Structures]]
[[Category: Iwashita, C]]
[[Category: Morita, D]]
[[Category: Sugita, M]]