5vge - Revision history

OCA at 13:48, 4 October 2023

2023-10-04T13:48:23Z

←Older revision		Revision as of 13:48, 4 October 2023
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	==Crystal structure of HLA-C*07:02 in complex with RYR peptide==		==Crystal structure of HLA-C*07:02 in complex with RYR peptide==
-	<StructureSection load='5vge' size='340' side='right' caption='[[5vge]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5vge' size='340' side='right'caption='[[5vge]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vge]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VGE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VGE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vge]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VGE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ZN:ZINC+ION'>ZN</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]] 2.6Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5vgd\|5vgd]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">B2M, CDABP0092, HDCMA22P ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=5vge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vge OCA], [https://pdbe.org/5vge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vge RCSB], [https://www.ebi.ac.uk/pdbsum/5vge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vge ProSAT]</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=5vge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vge OCA], [~~http~~://pdbe.org/5vge PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vge RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vge PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vge ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/~~B2MG_HUMAN B2MG_HUMAN~~]~~] Defects in B2M are the cause of hypercatabolic hypoproteinemia~~ (~~HYCATHYP~~) ~~[MIM:[http://omim~~.~~org/entry/241600 241600]]~~. ~~Affected individuals show marked reduction in serum concentrations of immunoglobulin and albumin, probably due to rapid degradation~~.~~<ref>PMID:16549777</ref> Note=Beta-2-microglobulin may adopt~~ the ~~fibrillar configuration of amyloid~~ in ~~certain pathologic states~~. ~~The capacity to assemble into amyloid fibrils is concentration dependent. Persistently high beta~~(2)~~-microglobulin serum levels lead~~ to ~~amyloidosis in patients~~ on ~~long~~-~~term hemodialysis~~.<ref>PMID:3532124</ref> <ref>PMID:1336137</ref> <ref>PMID:7554280</ref> <ref>PMID:4586824</ref> <ref>PMID:8084451</ref> <ref>PMID:12119416</ref> <ref>PMID:12796775</ref> <ref>PMID:16901902</ref> <ref>PMID:16491088</ref> <ref>PMID:17646174</ref> <ref>PMID:18835253</ref> <ref>PMID:18395224</ref> <ref>PMID:19284997</ref>	+	[https://www.uniprot.org/uniprot/HLAC_HUMAN HLAC_HUMAN] B-lymphoblastic leukemia/lymphoma with t(9;22)(q34.1;q11.2). Disease susceptibility is associated with variants affecting the gene represented in this entry. Allele C*06:02 presents a melanocyte autoantigen ADAMTSL5 (VRSRRCLRL) to Valpha3S1/Vbeta13S1 TCR on CD8-positive T cells, and may trigger an autoimmune response against melanocytes.<ref>PMID:26621454</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~B2MG_HUMAN B2MG_HUMAN~~]~~] 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/HLAC_HUMAN HLAC_HUMAN] Antigen-presenting major histocompatibility complex class I (MHCI) molecule with an important role in reproduction and antiviral immunity (PubMed:20972337, PubMed:24091323, PubMed:20439706, PubMed:11172028, PubMed:20104487, PubMed:28649982, PubMed:29312307). In complex with B2M/beta 2 microglobulin displays a restricted repertoire of self and viral peptides and acts as a dominant ligand for inhibitory and activating killer immunoglobulin receptors (KIRs) expressed on NK cells (PubMed:16141329). In an allogeneic setting, such as during pregnancy, mediates interaction of extravillous trophoblasts with KIR on uterine NK cells and regulate trophoblast invasion necessary for placentation and overall fetal growth (PubMed:20972337, PubMed:24091323). During viral infection, may present viral peptides with low affinity for KIRs, impeding KIR-mediated inhibition through peptide antagonism and favoring lysis of infected cells (PubMed:20439706). Presents a restricted repertoire of viral peptides on antigen-presenting cells for recognition by alpha-beta T cell receptor (TCR) on HLA-C-restricted CD8-positive T cells, guiding antigen-specific T cell immune response to eliminate infected cells, particularly in chronic viral infection settings such as HIV-1 or CMV infection (PubMed:11172028, PubMed:20104487, PubMed:28649982). Both the peptide and the MHC molecule are recognized by TCR, the peptide is responsible for the fine specificity of antigen recognition and MHC residues account for the MHC restriction of T cells (By similarity). Typically presents intracellular peptide antigens of 9 amino acids that arise from cytosolic proteolysis via proteasome. Can bind different peptides containing allele-specific binding motifs, which are mainly defined by anchor residues at position 2 and 9. Preferentially displays peptides having a restricted repertoire of hydrophobic or aromatic amino acids (Phe, Ile, Leu, Met, Val and Tyr) at the C-terminal anchor (PubMed:8265661, PubMed:25311805).[UniProtKB:P04439]<ref>PMID:11172028</ref> <ref>PMID:16141329</ref> <ref>PMID:20104487</ref> <ref>PMID:20439706</ref> <ref>PMID:20972337</ref> <ref>PMID:24091323</ref> <ref>PMID:25311805</ref> <ref>PMID:28649982</ref> <ref>PMID:29312307</ref> <ref>PMID:8265661</ref> ALLELE C01:02: The peptide-bound form interacts with KIR2DL2 and KIR2DL3 inhibitory receptors on NK cells. The low affinity peptides compete with the high affinity peptides impeding KIR-mediated inhibition and favoring lysis of infected cells (PubMed:20439706). Presents to CD8-positive T cells a CMV epitope derived from UL83/pp65 (RCPEMISVL), an immediate-early antigen necessary for initiating viral replication (PubMed:12947002).<ref>PMID:12947002</ref> <ref>PMID:20439706</ref> ALLELE C04:01: Presents a conserved HIV-1 epitope derived from env (SFNCGGEFF) to memory CD8-positive T cells, eliciting very strong IFNG responses (PubMed:20104487). Presents CMV epitope derived from UL83/pp65 (QYDPVAALF) to CD8-positive T cells, triggering T cell cytotoxic response (PubMed:12947002).<ref>PMID:12947002</ref> <ref>PMID:20104487</ref> ALLELE C05:01: Presents HIV-1 epitope derived from rev (SAEPVPLQL) to CD8-positive T cells, triggering T cell cytotoxic response.<ref>PMID:11172028</ref> ALLELE C06:02: In trophoblasts, interacts with KIR2DS2 on uterine NK cells and triggers NK cell activation, including secretion of cytokines such as GMCSF that enhances trophoblast migration.<ref>PMID:24091323</ref> ALLELE C07:02: Plays an important role in the control of chronic CMV infection. Presents immunodominant CMV epitopes derived from IE1 (LSEFCRVL and CRVLCCYVL) and UL28 (FRCPRRFCF), both antigens synthesized during immediate-early period of viral replication. Elicits a strong anti-viral CD8-positive T cell immune response that increases markedly with age.<ref>PMID:29312307</ref> ALLELE C08:01: Presents viral epitopes derived from CMV UL83 (VVCAHELVC) and IAV M1 (GILGFVFTL), triggering CD8-positive T cell cytotoxic response.<ref>PMID:12947002</ref> <ref>PMID:24990997</ref> ALLELE C12:02: Presents CMV epitope derived from UL83 (VAFTSHEHF) to CD8-positive T cells.<ref>PMID:12947002</ref> ALLELE C15:02: Presents CMV epitope derived from UL83 CC (VVCAHELVC) to CD8-positive T cells, triggering T cell cytotoxic response.<ref>PMID:12947002</ref>
	<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 5vge" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vge" 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: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Gras, S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Mobbs, J I~~]]	+	[[Category: Gras S]]
-	[[Category: ~~Rossjohn, J~~]]	+	[[Category: Mobbs JI]]
-	[[Category: ~~Vivian,~~ J P]]	+	[[Category: Rossjohn J]]
-	[[Category: ~~Human leukocyte antigen major histocompatibility complex antigen presentation]]~~	+	[[Category: Vivian JP]]
-	~~[[Category: Immune system~~]]	+

OCA at 11:00, 16 November 2017

2017-11-16T11:00:06Z

←Older revision		Revision as of 11:00, 16 November 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5vge is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of HLA-C*07:02 in complex with RYR peptide==
		+	<StructureSection load='5vge' size='340' side='right' caption='[[5vge]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vge]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VGE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vgd\|5vgd]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B2M, CDABP0092, HDCMA22P ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5vge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vge OCA], [http://pdbe.org/5vge PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vge RCSB], [http://www.ebi.ac.uk/pdbsum/5vge PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vge ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN]] Defects in B2M are the cause of hypercatabolic hypoproteinemia (HYCATHYP) [MIM:[http://omim.org/entry/241600 241600]]. Affected individuals show marked reduction in serum concentrations of immunoglobulin and albumin, probably due to rapid degradation.<ref>PMID:16549777</ref> Note=Beta-2-microglobulin may adopt the fibrillar configuration of amyloid in certain pathologic states. The capacity to assemble into amyloid fibrils is concentration dependent. Persistently high beta(2)-microglobulin serum levels lead to amyloidosis in patients on long-term hemodialysis.<ref>PMID:3532124</ref> <ref>PMID:1336137</ref> <ref>PMID:7554280</ref> <ref>PMID:4586824</ref> <ref>PMID:8084451</ref> <ref>PMID:12119416</ref> <ref>PMID:12796775</ref> <ref>PMID:16901902</ref> <ref>PMID:16491088</ref> <ref>PMID:17646174</ref> <ref>PMID:18835253</ref> <ref>PMID:18395224</ref> <ref>PMID:19284997</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN]] 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 ==
		+	Expression of HLA-C varies widely across individuals in an allele-specific manner. This variation in expression can influence efficacy of the immune response, as shown for infectious and autoimmune diseases. MicroRNA binding partially influences differential HLA-C expression, but the additional contributing factors have remained undetermined. Here we use functional and structural analyses to demonstrate that HLA-C expression is modulated not just at the RNA level, but also at the protein level. Specifically, we show that variation in exons 2 and 3, which encode the alpha1/alpha2 domains, drives differential expression of HLA-C allomorphs at the cell surface by influencing the structure of the peptide-binding cleft and the diversity of peptides bound by the HLA-C molecules. Together with a phylogenetic analysis, these results highlight the diversity and long-term balancing selection of regulatory factors that modulate HLA-C expression.

-	~~Authors~~:	+	Structural and regulatory diversity shape HLA-C protein expression levels.,Kaur G, Gras S, Mobbs JI, Vivian JP, Cortes A, Barber T, Kuttikkatte SB, Jensen LT, Attfield KE, Dendrou CA, Carrington M, McVean G, Purcell AW, Rossjohn J, Fugger L Nat Commun. 2017 Jun 26;8:15924. doi: 10.1038/ncomms15924. PMID:28649982<ref>PMID:28649982</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5vge" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Gras, S]]
		+	[[Category: Mobbs, J I]]
		+	[[Category: Rossjohn, J]]
		+	[[Category: Vivian, J P]]
		+	[[Category: Human leukocyte antigen major histocompatibility complex antigen presentation]]
		+	[[Category: Immune system]]

OCA at 11:30, 24 May 2017

2017-05-24T11:30:42Z

←Older revision		Revision as of 11:30, 24 May 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2017-04-19T11:24:43Z

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

←Older revision

Revision as of 11:24, 19 April 2017

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

2017-04-19T11:24:42Z

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

New page

'''Unreleased structure'''

The entry 5vge is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]