3vfp - Revision history

OCA at 14:27, 14 March 2024

OCA — Thu, 14 Mar 2024 14:27:35 GMT

←Older revision		Revision as of 14:27, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3vfp' size='340' side='right'caption='[[3vfp]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3vfp' size='340' side='right'caption='[[3vfp]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vfp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human ~~Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VFP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vfp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_herpesvirus_4_strain_B95-8 Human herpesvirus 4 strain B95-8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VFP FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</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]] 1.85Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1zhk\|1zhk]]~~, [[~~1zhl~~\|~~1zhl]], [[2ak4\|2ak4]], [[3vfm\|3vfm]], [[3vfn\|3vfn]], [[3vfo\|3vfo]], [[3vfr\|3vfr]], [[3vfs\|3vfs]], [[3vft\|3vft]], [[3vfu\|3vfu]], [[3vfv\|3vfv]], [[3vfw\|3vfw~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~HLA-B ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]), B2M, CDABP0092, HDCMA22P ([https~~:/~~/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=3vfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfp OCA], [https://pdbe.org/3vfp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vfp RCSB], [https://www.ebi.ac.uk/pdbsum/3vfp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vfp 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=3vfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfp OCA], [https://pdbe.org/3vfp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vfp RCSB], [https://www.ebi.ac.uk/pdbsum/3vfp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vfp ProSAT]</span></td></tr>
	</table>		</table>
-	== Disease ==
-	[[https://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN]] Defects in B2M are the cause of hypercatabolic hypoproteinemia (HYCATHYP) [MIM:[https://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 ==		== Function ==
-	[[https://www.uniprot.org/uniprot/C5MK56_HUMAN C5MK56_HUMAN]] Involved in the presentation of foreign antigens to the immune system (By similarity).[SAAS:SAAS003006_004_004364] ~~[[https://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/C5MK56_HUMAN C5MK56_HUMAN] Involved in the presentation of foreign antigens to the immune system (By similarity).[SAAS:SAAS003006_004_004364]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	While the Major Histocompatibility Complex Class I (MHC-I) molecules typically bind short peptide (p) fragments (8-10 amino acids in length), longer, bulged, peptides are often be presented by MHC-I. Such bulged pMHC-I complexes represent challenges for T-cell receptor (TCR) ligation, although the general principles underscoring the interaction between TCRs and bulged pMHC-I complexes are unclear. To address this, we have explored the energetic basis of how an immunodominant TCR (termed SB27) binds to a 13 amino acid viral peptide (LPEPLPQGQLTAY) complexed to Human Leukocyte Antigen (HLA) B3508. Using the crystal structure of the SB27 TCR-HLA B3508LPEP complex as a guide, we undertook a comprehensive alanine-scanning mutagenesis approach at the TCR-pMHC-I interface and examined the effect of the mutations by biophysical (affinity measurements) and cellular approaches (tetramer staining). While the structural footprint on the HLA B3508 was small, the energetic footprint was even smaller in that only two HLA B3508 residues were critical for the TCR interaction. Instead, the energetic basis of this TCR-pMHC-I interaction was attributed to peptide-mediated interactions in which the complementarity determining region (CDR) 3alpha and germline encoded CDR1beta loops of the SB27 TCR played the principal role. Our findings highlight the peptide-centricity of TCR ligation towards a bulged pMHC-I complex.	+
-		+
-	The energetic basis underpinning T-cell teceptor tecognition of a super-bulged peptide bound to a major histocompatibility complex class I molecule.,Liu YC, Chen Z, Burrows SR, Purcell AW, McCluskey J, Rossjohn J, Gras S J Biol Chem. 2012 Feb 16. PMID:22343629<ref>PMID:22343629</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3vfp" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]		*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human]]	+	[[Category: Homo sapiens]]
		+	[[Category: Human herpesvirus 4 strain B95-8]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gras, S]]	+	[[Category: Gras S]]
-	[[Category: Liu~~, Y C~~]]	+	[[Category: Liu YC]]
-	[[Category: Rossjohn, J]]	+	[[Category: Rossjohn J]]
-	~~[[Category: Antigen-presenting molecule]]~~	+
-	~~[[Category: Epstein barr virus]]~~	+
-	~~[[Category: Hla b*3508]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: T cell]]~~	+
-	~~[[Category: Tcr~~]]	+

OCA at 18:43, 27 July 2022

OCA — Wed, 27 Jul 2022 18:43:05 GMT

←Older revision		Revision as of 18:43, 27 July 2022
Line 1:		Line 1:

	==crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158==		==crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158==
-	<StructureSection load='3vfp' size='340' side='right' caption='[[3vfp]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='3vfp' size='340' side='right'caption='[[3vfp]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vfp]] 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=3VFP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VFP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vfp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VFP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zhk\|1zhk]], [[1zhl\|1zhl]], [[2ak4\|2ak4]], [[3vfm\|3vfm]], [[3vfn\|3vfn]], [[3vfo\|3vfo]], [[3vfr\|3vfr]], [[3vfs\|3vfs]], [[3vft\|3vft]], [[3vfu\|3vfu]], [[3vfv\|3vfv]], [[3vfw\|3vfw]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1zhk\|1zhk]], [[1zhl\|1zhl]], [[2ak4\|2ak4]], [[3vfm\|3vfm]], [[3vfn\|3vfn]], [[3vfo\|3vfo]], [[3vfr\|3vfr]], [[3vfs\|3vfs]], [[3vft\|3vft]], [[3vfu\|3vfu]], [[3vfv\|3vfv]], [[3vfw\|3vfw]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HLA-B ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), B2M, CDABP0092, HDCMA22P ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HLA-B ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), B2M, CDABP0092, HDCMA22P ([https://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=3vfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfp OCA], [~~http~~://pdbe.org/3vfp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vfp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vfp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vfp 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=3vfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfp OCA], [https://pdbe.org/3vfp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vfp RCSB], [https://www.ebi.ac.uk/pdbsum/3vfp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vfp 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/B2MG_HUMAN B2MG_HUMAN]] Defects in B2M are the cause of hypercatabolic hypoproteinemia (HYCATHYP) [MIM:[https://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 ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/C5MK56_HUMAN C5MK56_HUMAN]] Involved in the presentation of foreign antigens to the immune system (By similarity).[SAAS:SAAS003006_004_004364] [[~~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/C5MK56_HUMAN C5MK56_HUMAN]] Involved in the presentation of foreign antigens to the immune system (By similarity).[SAAS:SAAS003006_004_004364] [[https://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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:

	==See Also==		==See Also==
-	*[[Beta-2 microglobulin\|Beta-2 microglobulin]]	+	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Gras, S]]		[[Category: Gras, S]]
	[[Category: Liu, Y C]]		[[Category: Liu, Y C]]

OCA at 19:12, 10 December 2016

OCA — Sat, 10 Dec 2016 19:12:21 GMT

←Older revision		Revision as of 19:12, 10 December 2016
Line 1:		Line 1:
		+
	==crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158==		==crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158==
	<StructureSection load='3vfp' size='340' side='right' caption='[[3vfp]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3vfp' size='340' side='right' caption='[[3vfp]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vfp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VFP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vfp]] 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=3VFP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VFP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zhk\|1zhk]], [[1zhl\|1zhl]], [[2ak4\|2ak4]], [[3vfm\|3vfm]], [[3vfn\|3vfn]], [[3vfo\|3vfo]], [[3vfr\|3vfr]], [[3vfs\|3vfs]], [[3vft\|3vft]], [[3vfu\|3vfu]], [[3vfv\|3vfv]], [[3vfw\|3vfw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zhk\|1zhk]], [[1zhl\|1zhl]], [[2ak4\|2ak4]], [[3vfm\|3vfm]], [[3vfn\|3vfn]], [[3vfo\|3vfo]], [[3vfr\|3vfr]], [[3vfs\|3vfs]], [[3vft\|3vft]], [[3vfu\|3vfu]], [[3vfv\|3vfv]], [[3vfw\|3vfw]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HLA-B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), B2M, CDABP0092, HDCMA22P ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HLA-B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), 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=3vfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vfp RCSB], [http://www.ebi.ac.uk/pdbsum/3vfp PDBsum]</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=3vfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfp OCA], [http://pdbe.org/3vfp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vfp RCSB], [http://www.ebi.ac.uk/pdbsum/3vfp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vfp ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 21:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3vfp" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 27:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Gras, S]]		[[Category: Gras, S]]
	[[Category: Liu, Y C]]		[[Category: Liu, Y C]]

OCA at 08:36, 15 February 2015

OCA — Sun, 15 Feb 2015 08:36:34 GMT

←Older revision		Revision as of 08:36, 15 February 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3vfp~~\| ~~PDB~~=3vfp \| ~~SCENE~~= }}	+	==crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158==
-	===crystal structure of HLA B*3508 ~~LPEP158G~~, HLA ~~mutant Gly158===~~	+	<StructureSection load='3vfp' size='340' side='right' caption='[[3vfp]], [[Resolution\|resolution]] 1.85Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22343629}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3vfp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VFP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zhk\|1zhk]], [[1zhl\|1zhl]], [[2ak4\|2ak4]], [[3vfm\|3vfm]], [[3vfn\|3vfn]], [[3vfo\|3vfo]], [[3vfr\|3vfr]], [[3vfs\|3vfs]], [[3vft\|3vft]], [[3vfu\|3vfu]], [[3vfv\|3vfv]], [[3vfw\|3vfw]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HLA-B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), B2M, CDABP0092, HDCMA22P ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3vfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vfp RCSB], [http://www.ebi.ac.uk/pdbsum/3vfp PDBsum]</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/C5MK56_HUMAN C5MK56_HUMAN]] Involved in the presentation of foreign antigens to the immune system (By similarity).[SAAS:SAAS003006_004_004364] [[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 ==
		+	While the Major Histocompatibility Complex Class I (MHC-I) molecules typically bind short peptide (p) fragments (8-10 amino acids in length), longer, bulged, peptides are often be presented by MHC-I. Such bulged pMHC-I complexes represent challenges for T-cell receptor (TCR) ligation, although the general principles underscoring the interaction between TCRs and bulged pMHC-I complexes are unclear. To address this, we have explored the energetic basis of how an immunodominant TCR (termed SB27) binds to a 13 amino acid viral peptide (LPEPLPQGQLTAY) complexed to Human Leukocyte Antigen (HLA) B3508. Using the crystal structure of the SB27 TCR-HLA B3508LPEP complex as a guide, we undertook a comprehensive alanine-scanning mutagenesis approach at the TCR-pMHC-I interface and examined the effect of the mutations by biophysical (affinity measurements) and cellular approaches (tetramer staining). While the structural footprint on the HLA B3508 was small, the energetic footprint was even smaller in that only two HLA B3508 residues were critical for the TCR interaction. Instead, the energetic basis of this TCR-pMHC-I interaction was attributed to peptide-mediated interactions in which the complementarity determining region (CDR) 3alpha and germline encoded CDR1beta loops of the SB27 TCR played the principal role. Our findings highlight the peptide-centricity of TCR ligation towards a bulged pMHC-I complex.

-	~~==Disease==~~	+	The energetic basis underpinning T-cell teceptor tecognition of a super-bulged peptide bound to a major histocompatibility complex class I molecule.,Liu YC, Chen Z, Burrows SR, Purcell AW, McCluskey J, Rossjohn J, Gras S J Biol Chem. 2012 Feb 16. PMID:22343629<ref>PMID:22343629</ref>
-	~~[[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==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~/~~/www.uniprot.org/uniprot/C5MK56_HUMAN C5MK56_HUMAN]] Involved in the presentation~~ of ~~foreign antigens to~~ the ~~immune system (By similarity)~~.~~[SAAS:SAAS003006_004_004364] [[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>
-		+
-	~~==About this Structure==~~	+
-	~~[[3vfp]] is a 3 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFP OCA].~~	+

	==See Also==		==See Also==
	*[[Beta-2 microglobulin\|Beta-2 microglobulin]]		*[[Beta-2 microglobulin\|Beta-2 microglobulin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:022343629</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Gras, S.]]	+	[[Category: Gras, S]]
-	[[Category: Liu, Y C.]]	+	[[Category: Liu, Y C]]
-	[[Category: Rossjohn, J.]]	+	[[Category: Rossjohn, J]]
	[[Category: Antigen-presenting molecule]]		[[Category: Antigen-presenting molecule]]
	[[Category: Epstein barr virus]]		[[Category: Epstein barr virus]]

OCA at 01:25, 25 March 2013

OCA — Mon, 25 Mar 2013 01:25:58 GMT

←Older revision		Revision as of 01:25, 25 March 2013
Line 1:		Line 1:
-	[[Image:3vfp.png\|left\|200px]]
-
	{{STRUCTURE_3vfp\| PDB=3vfp \| SCENE= }}		{{STRUCTURE_3vfp\| PDB=3vfp \| SCENE= }}
-
	===crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158===		===crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158===
		+	{{ABSTRACT_PUBMED_22343629}}

-	~~{{ABSTRACT_PUBMED_22343629}}~~	+	==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/C5MK56_HUMAN C5MK56_HUMAN]] Involved in the presentation of foreign antigens to the immune system (By similarity).[SAAS:SAAS003006_004_004364] [[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.

	==About this Structure==		==About this Structure==
Line 14:		Line 16:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:022343629</ref><references group="xtra"/>	+	<ref group="xtra">PMID:022343629</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Gras, S.]]		[[Category: Gras, S.]]

OCA at 16:38, 20 October 2012

OCA — Sat, 20 Oct 2012 16:38:39 GMT

←Older revision		Revision as of 16:38, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3vfp]] is a 3 chain structure ~~of [[Beta-2 microglobulin]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFP OCA].	+	[[3vfp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFP OCA].

	==See Also==		==See Also==

OCA at 04:35, 8 August 2012

OCA — Wed, 08 Aug 2012 04:35:48 GMT

←Older revision		Revision as of 04:35, 8 August 2012
Line 3:		Line 3:
	{{STRUCTURE_3vfp\| PDB=3vfp \| SCENE= }}		{{STRUCTURE_3vfp\| PDB=3vfp \| SCENE= }}

-	===~~Crystal Structure~~ of ~~peptide-~~HLA ~~complex~~, HLA mutant===	+	===crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158===

	{{ABSTRACT_PUBMED_22343629}}		{{ABSTRACT_PUBMED_22343629}}

OCA at 22:21, 26 July 2012

OCA — Thu, 26 Jul 2012 22:21:17 GMT

←Older revision		Revision as of 22:21, 26 July 2012
Line 1:		Line 1:
	[[Image:3vfp.png\|left\|200px]]		[[Image:3vfp.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3vfp", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3vfp\| PDB=3vfp \| SCENE= }}		{{STRUCTURE_3vfp\| PDB=3vfp \| SCENE= }}

	===Crystal Structure of peptide-HLA complex, HLA mutant===		===Crystal Structure of peptide-HLA complex, HLA mutant===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22343629}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22343629 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22343629}}		{{ABSTRACT_PUBMED_22343629}}

	==About this Structure==		==About this Structure==
-	[[3vfp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFP OCA].	+	[[3vfp]] is a 3 chain structure of [[Beta-2 microglobulin]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFP OCA].
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin\|Beta-2 microglobulin]]

	==Reference==		==Reference==

OCA at 08:30, 25 April 2012

OCA — Wed, 25 Apr 2012 08:30:46 GMT

←Older revision		Revision as of 08:30, 25 April 2012
Line 1:		Line 1:
-	[[Image:3vfp.~~jpg~~\|left\|200px]]	+	[[Image:3vfp.png\|left\|200px]]

	<!--		<!--

OCA at 05:49, 8 March 2012

OCA — Thu, 08 Mar 2012 05:49:27 GMT

←Older revision		Revision as of 05:49, 8 March 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3vfp.jpg\|left\|200px]]

-	The ~~entry 3vfp~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3vfp", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3vfp\| PDB=3vfp \| SCENE= }}

-	~~Authors: Liu~~, ~~Y.C., Rossjohn, J., Gras, S.~~	+	===Crystal Structure of peptide-HLA complex, HLA mutant===

-	~~Description~~: ~~Crystal~~ Structure ~~of peptide~~-~~HLA complex~~, ~~HLA mutant~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22343629}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22343629 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22343629}}
		+
		+	==About this Structure==
		+	[[3vfp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFP OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022343629</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Gras, S.]]
		+	[[Category: Liu, Y C.]]
		+	[[Category: Rossjohn, J.]]
		+	[[Category: Antigen-presenting molecule]]
		+	[[Category: Epstein barr virus]]
		+	[[Category: Hla b*3508]]
		+	[[Category: Immune system]]
		+	[[Category: T cell]]
		+	[[Category: Tcr]]