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3vfr

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crystal structure of HLA B*3508LPEP-P4Ala, peptide mutant P4-ala

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 ==crystal structure of HLA B*3508LPEP-P4Ala, peptide mutant P4-ala==
-<StructureSection load='3vfr' size='340' side='right' caption='[[3vfr]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='3vfr' size='340' side='right'caption='[[3vfr]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3vfr]] 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=3VFR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VFR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3vfr]] 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=3VFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VFR FirstGlance]. <br>
-</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]], [[3vfp|3vfp]], [[3vfs|3vfs]], [[3vft|3vft]], [[3vfu|3vfu]], [[3vfv|3vfv]], [[3vfw|3vfw]]</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]] 1.85&#8491;</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'>[https://proteopedia.org/fgij/fg.htm?mol=3vfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfr OCA], [https://pdbe.org/3vfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vfr RCSB], [https://www.ebi.ac.uk/pdbsum/3vfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vfr 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=3vfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfr OCA], [http://pdbe.org/3vfr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vfr RCSB], [http://www.ebi.ac.uk/pdbsum/3vfr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vfr 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/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]
-<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) B*3508. Using the crystal structure of the SB27 TCR-HLA B*3508LPEP 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 B*3508 was small, the energetic footprint was even smaller in that only two HLA B*3508 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3vfr" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Beta-2 microglobulin|Beta-2 microglobulin]]
+*[[Beta-2 microglobulin 3D structures|Beta-2 microglobulin 3D structures]]
-== References ==
+*[[MHC 3D structures|MHC 3D structures]]
-<references/>
+*[[MHC I 3D structures|MHC I 3D structures]]
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Gras, S]]
+[[Category: Human herpesvirus 4 strain B95-8]]
-[[Category: Liu, Y C]]
+[[Category: Large Structures]]
-[[Category: Rossjohn, J]]
+[[Category: Gras S]]
-[[Category: Antigen-presenting molecule]]
+[[Category: Liu YC]]
-[[Category: Epstein barr virus]]
+[[Category: Rossjohn J]]
-[[Category: Hla b*3508]]
-[[Category: Immune system]]
-[[Category: T cell]]
-[[Category: Tcr]]

3vfr

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crystal structure of HLA B*3508LPEP-P4Ala, peptide mutant P4-ala

Structural highlights

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