6iwg - Revision history

OCA at 09:54, 22 November 2023

OCA — Wed, 22 Nov 2023 09:54:22 GMT

←Older revision		Revision as of 09:54, 22 November 2023
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	<StructureSection load='6iwg' size='340' side='right'caption='[[6iwg]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6iwg' size='340' side='right'caption='[[6iwg]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6iwg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IWG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IWG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6iwg]] is a 3 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=6IWG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IWG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BO3:BORIC+ACID'>BO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:~~SODIUM~~+~~ION~~'>NA</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]] 1.8Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~MYR~~:~~MYRISTIC~~+~~ACID~~'>~~MYR~~</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BO3:BORIC+ACID'>BO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6iwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iwg OCA], [~~http~~://pdbe.org/6iwg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6iwg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6iwg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6iwg 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=6iwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iwg OCA], [https://pdbe.org/6iwg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iwg RCSB], [https://www.ebi.ac.uk/pdbsum/6iwg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iwg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~B2MG_MACMU B2MG_MACMU~~]~~] Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system (By similarity).~~	+	[https://www.uniprot.org/uniprot/B2ZHY7_MACMU B2ZHY7_MACMU]
	<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 6iwg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6iwg" 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]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Morita, D~~]]	+	[[Category: Macaca mulatta]]
-	[[Category: ~~Sugita, M~~]]	+	[[Category: Simian immunodeficiency virus]]
-	[[Category: ~~Yamamoto, Y~~]]	+	[[Category: Morita D]]
-	[[Category: ~~Aid~~]]	+	[[Category: Sugita M]]
-	[[Category: ~~Antigen presentation]]~~	+	[[Category: Yamamoto Y]]
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Major histocompatibility complex]]~~	+
-	~~[[Category: N-myristoylation]]~~	+
-	~~[[Category: Nef~~]]	+

OCA at 16:32, 14 August 2019

OCA — Wed, 14 Aug 2019 16:32:24 GMT

←Older revision		Revision as of 16:32, 14 August 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6iwg is ~~ON HOLD~~	+	==Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with N-myristoylated 4-mer lipopeptide derived from SIV nef protein==
		+	<StructureSection load='6iwg' size='340' side='right'caption='[[6iwg]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6iwg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IWG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IWG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BO3:BORIC+ACID'>BO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</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=6iwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iwg OCA], [http://pdbe.org/6iwg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iwg RCSB], [http://www.ebi.ac.uk/pdbsum/6iwg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iwg ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/B2MG_MACMU B2MG_MACMU]] Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Similar to host proteins, N-myristoylation occurs for viral proteins to dictate their pathological function. However, this lipid-modifying reaction creates a novel class of "lipopeptide" Ags targeted by host CTLs. The primate MHC class I-encoded protein, Mamu-B098, was previously shown to bind N-myristoylated 5-mer peptides. Nevertheless, T cells exist that recognize even shorter lipopeptides, and much remains to be elucidated concerning the molecular mechanisms of lipopeptide presentation. We, in this study, demonstrate that the MHC class I allele, Mamu-B05104, binds the N-myristoylated 4-mer peptide (C14-Gly-Gly-Ala-Ile) derived from the viral Nef protein for its presentation to CTLs. A phylogenetic tree analysis indicates that these classical MHC class I alleles are not closely associated; however, the high-resolution x-ray crystallographic analyses indicate that both molecules share lipid-binding structures defined by the exceptionally large, hydrophobic B pocket to accommodate the acylated glycine (G1) as an anchor. The C-terminal isoleucine (I4) of C14-Gly-Gly-Ala-Ile anchors at the F pocket, which is distinct from that of Mamu-B*098 and is virtually identical to that of the peptide-presenting MHC class I molecule, HLA-B51. The two central amino acid residues (G2 and A3) are only exposed externally for recognition by T cells, and the methyl side chain on A3 constitutes a major T cell epitope, underscoring that the epitopic diversity is highly limited for lipopeptides as compared with that for MHC class I-presented long peptides. These structural features suggest that lipopeptide-presenting MHC class I alleles comprise a distinct MHC class I subset that mediates an alternative pathway for CTL activation.

-	~~Authors: Yamamoto~~, Y., Morita, D., ~~Sugita~~, M.	+	Identification and Structure of an MHC Class I-Encoded Protein with the Potential to Present N-Myristoylated 4-mer Peptides to T Cells.,Yamamoto Y, Morita D, Shima Y, Midorikawa A, Mizutani T, Suzuki J, Mori N, Shiina T, Inoko H, Tanaka Y, Mikami B, Sugita M J Immunol. 2019 Jun 15;202(12):3349-3358. doi: 10.4049/jimmunol.1900087. Epub, 2019 May 1. PMID:31043477<ref>PMID:31043477</ref>

-	~~Description: Crystal structure~~ of ~~rhesus macaque MHC~~ class ~~I molecule Mamu~~-~~B*05104 complexed with N~~-~~myristoylated 4-mer lipopeptide derived from SIV nef protein~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6iwg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Morita, D]]		[[Category: Morita, D]]
	[[Category: Sugita, M]]		[[Category: Sugita, M]]
	[[Category: Yamamoto, Y]]		[[Category: Yamamoto, Y]]
		+	[[Category: Aid]]
		+	[[Category: Antigen presentation]]
		+	[[Category: Immune system]]
		+	[[Category: Major histocompatibility complex]]
		+	[[Category: N-myristoylation]]
		+	[[Category: Nef]]

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

OCA — Wed, 12 Dec 2018 05:15:19 GMT

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

←Older revision

Revision as of 05:15, 12 December 2018

OCA: New page: '''Unreleased structure''' The entry 6iwg is ON HOLD Authors: Yamamoto, Y., Morita, D., Sugita, M. Description: Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 co...

OCA — Wed, 12 Dec 2018 05:15:18 GMT

New page: '''Unreleased structure''' The entry 6iwg is ON HOLD Authors: Yamamoto, Y., Morita, D., Sugita, M. Description: Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 co...

New page

'''Unreleased structure'''

The entry 6iwg is ON HOLD

Authors: Yamamoto, Y., Morita, D., Sugita, M.

Description: Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with N-myristoylated 4-mer lipopeptide derived from SIV nef protein
[[Category: Unreleased Structures]]
[[Category: Morita, D]]
[[Category: Sugita, M]]
[[Category: Yamamoto, Y]]