4qrr - Revision history

OCA at 17:36, 20 September 2023

OCA — Wed, 20 Sep 2023 17:36:16 GMT

←Older revision		Revision as of 17:36, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qrr]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_herpesvirus_5_strain_Towne Human herpesvirus 5 strain Towne]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QRR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qrr]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_herpesvirus_5_strain_Towne Human herpesvirus 5 strain Towne]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QRR 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=4qrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qrr OCA], [https://pdbe.org/4qrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qrr RCSB], [https://www.ebi.ac.uk/pdbsum/4qrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qrr 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]] 3Å</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=4qrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qrr OCA], [https://pdbe.org/4qrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qrr RCSB], [https://www.ebi.ac.uk/pdbsum/4qrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qrr ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 13:49, 22 February 2023

OCA — Wed, 22 Feb 2023 13:49:33 GMT

←Older revision		Revision as of 13:49, 22 February 2023
Line 3:		Line 3:
	<StructureSection load='4qrr' size='340' side='right'caption='[[4qrr]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4qrr' size='340' side='right'caption='[[4qrr]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qrr]] is a 5 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=4QRR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=4QRR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qrr]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_herpesvirus_5_strain_Towne Human herpesvirus 5 strain Towne]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QRR FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qrp\|4qrp]], [[4qrq\|4qrq]], [[4qrs\|4qrs]], [[4qrt\|4qrt]]</td></tr>~~	+	</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=4qrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qrr OCA], [https://pdbe.org/4qrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qrr RCSB], [https://www.ebi.ac.uk/pdbsum/4qrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qrr ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HLA-B, HLAB ([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~~://proteopedia.org/fgij/fg.htm?mol=4qrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qrr OCA], [~~http~~://pdbe.org/4qrr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qrr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qrr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qrr 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/HLAB_HUMAN HLAB_HUMAN] Prediction of allopurinol toxicity;NON RARE IN EUROPE: Ankylosing spondylitis;Prediction of flucloxacilline toxicity;Giant cell arteritis;Takayasu arteritis;Reactive arthritis;Behcet disease;Stevens-Johnson syndrome;Prediction of phenytoin or carbamazepine toxicity;Pulmonary arterial hypertension associated with connective tissue disease;Prediction of abacavir toxicity. Disease susceptibility is associated with variants affecting the gene represented in this entry. Increased susceptibility to Stevens-Johnson syndrome is conferred by allele B15:02.<ref>PMID:15057820</ref> Disease susceptibility is associated with variants affecting the gene represented in this entry. A restricted number of HLA-B27 subtypes can be associated with ankylosing spondylitis and other B27-related diseases, and an elevated frequency of the B27:02 allele in ankylosing spondylitis patients is identified. The allele B27:07 seems to have a protective role in some populations because it was found only in the healthy controls.<ref>PMID:15603872</ref> There is evidence that HLA-B51 is associated with susceptibility to Behcet disease (BD). However, it is not certain whether HLA-B51 itself or a closely linked gene is responsible for susceptibility. The world distribution of HLA-B51 in healthy people corresponds to the global distribution of BD; in Southern hemisphere countries (Africa, South Pacific, etc.) and in some parts of Europe, the prevalence of HLA-B51 in healthy people is low or null, corresponding to a low prevalence of BD. The wide variation that exists in the relative risk of HLA-B51 would support other nongenetic risk factors.<ref>PMID:23291587</ref> The presence of allele B57:01 is associated with increased susceptibility to abacavir hypersensitivity [MIM:[https://omim.org/entry/142830 142830] in HIV-1 patients.<ref>PMID:11888582</ref> Allele group B08 is associated with increased susceptibility to rheumatoid arthritis, where affected individuals have antibodies to cyclic citrullinated peptide (anti-CCP-positive rheumatoid arthritis).<ref>PMID:22286218</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~1B35_HUMAN 1B35_HUMAN~~]~~] Involved in~~ the ~~presentation~~ of ~~foreign~~ antigens to the ~~immune system~~. ~~[[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~~. ~~[[http~~://~~www~~.~~uniprot~~.~~org~~/~~uniprot~~/~~PP65_HCMVT PP65_HCMVT]] Forms part of~~ the ~~matrix of~~ the ~~HCMV virion~~.	+	[https://www.uniprot.org/uniprot/HLAB_HUMAN HLAB_HUMAN] Antigen-presenting major histocompatibility complex class I (MHCI) molecule. In complex with B2M/beta 2 microglobulin displays primarily viral and tumor-derived peptides on antigen-presenting cells for recognition by alpha-beta T cell receptor (TCR) on HLA-B-restricted CD8-positive T cells, guiding antigen-specific T cell immune response to eliminate infected or transformed cells (PubMed:25808313, PubMed:29531227, PubMed:9620674, PubMed:23209413). May also present self-peptides derived from the signal sequence of secreted or membrane proteins, although T cells specific for these peptides are usually inactivated to prevent autoreactivity (PubMed:7743181, PubMed:18991276). 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 (PubMed:29531227, PubMed:9620674, PubMed:24600035). Typically presents intracellular peptide antigens of 8 to 13 amino acids that arise from cytosolic proteolysis via constitutive proteasome and IFNG-induced immunoproteasome (PubMed:23209413). Can bind different peptides containing allele-specific binding motifs, which are mainly defined by anchor residues at position 2 and 9 (PubMed:25808313, PubMed:29531227).<ref>PMID:18991276</ref> <ref>PMID:23209413</ref> <ref>PMID:24600035</ref> <ref>PMID:25808313</ref> <ref>PMID:29531227</ref> <ref>PMID:7743181</ref> <ref>PMID:9620674</ref> Allele B07:02: Displays peptides sharing a common signature motif, namely a Pro residue at position 2 and mainly a Leu anchor residue at the C-terminus (PubMed:7743181). Presents a long peptide (APRGPHGGAASGL) derived from the cancer-testis antigen CTAG1A/NY-ESO-1, eliciting a polyclonal CD8-positive T cell response against tumor cells (PubMed:29531227). Presents viral epitopes derived from HIV-1 gag-pol (TPQDLNTML) and Nef (RPQVPLRPM) (PubMed:25808313). Presents an immunodominant epitope derived from SARS-CoV-2 N/nucleoprotein (SPRWYFYYL) (PubMed:32887977). Displays self-peptides including a peptide derived from the signal sequence of HLA-DPB1 (APRTVALTA) (PubMed:7743181).<ref>PMID:25808313</ref> <ref>PMID:29531227</ref> <ref>PMID:32887977</ref> <ref>PMID:7743181</ref> Allele B08:01: Presents to CD8-positive T cells viral epitopes derived from EBV/HHV-4 EBNA3 (QAKWRLQTL), eliciting cytotoxic T cell response.<ref>PMID:9620674</ref> Allele B13:02: Presents multiple HIV-1 epitopes derived from gag (RQANFLGKI, GQMREPRGSDI), nef (RQDILDLWI), gag-pol (RQYDQILIE, GQGQWTYQI) and rev (LQLPPLERL), all having in common a Gln residue at position 2 and mainly hydrophobic amino acids Leu, Ile or Val at the C-terminus. Associated with succesful control of HIV-1 infection.<ref>PMID:17251285</ref> Allele B18:01: Preferentially presents octomeric and nonameric peptides sharing a common motif, namely a Glu at position 2 and Phe or Tyr anchor residues at the C-terminus (PubMed:14978097, PubMed:23749632, PubMed:18991276). Presents an EBV/HHV-4 epitope derived from BZLF1 (SELEIKRY) (PubMed:23749632). May present to CD8-positive T cells an antigenic peptide derived from MAGEA3 (MEVDPIGHLY), triggering an anti-tumor immune response (PubMed:12366779). May display a broad repertoire of self-peptides with a preference for peptides derived from RNA-binding proteins (PubMed:14978097).<ref>PMID:12366779</ref> <ref>PMID:14978097</ref> <ref>PMID:18991276</ref> <ref>PMID:23749632</ref> Allele B27:05: Presents to CD8-positive T cells immunodominant viral epitopes derived from HCV POLG (ARMILMTHF), HIV-1 gag (KRWIILGLNK), IAV NP (SRYWAIRTR), SARS-CoV-2 N/nucleoprotein (QRNAPRITF), EBV/HHV-4 EBNA4 (HRCQAIRKK) and EBV/HHV-4 EBNA6 (RRIYDLIEL), confering longterm protection against viral infection (PubMed:19139562, PubMed:18385228, PubMed:15113903, PubMed:9620674, PubMed:32887977). Can present self-peptides derived from cytosolic and nuclear proteins. All peptides carry an Arg at position 2 (PubMed:1922338). The peptide-bound form interacts with NK cell inhibitory receptor KIR3DL1 and inhibits NK cell activation in a peptide-specific way, being particularly sensitive to the nature of the amino acid side chain at position 8 of the antigenic peptide (PubMed:8879234, PubMed:15657948). KIR3DL1 fails to recognize HLA-B27:05 in complex with B2M and EBV/HHV-4 EBNA6 (RRIYDLIEL) peptide, which can lead to increased activation of NK cells during infection (PubMed:15657948). May present an altered repertoire of peptides in the absence of TAP1-TAP2 and TAPBPL (PubMed:9620674).<ref>PMID:15113903</ref> <ref>PMID:15657948</ref> <ref>PMID:18385228</ref> <ref>PMID:19139562</ref> <ref>PMID:1922338</ref> <ref>PMID:8879234</ref> <ref>PMID:9620674</ref> Allele B40:01: Presents immunodominant viral epitopes derived from EBV/HHV-4 LMP2 (IEDPPFNSL) and SARS-CoV-2 N/nucleoprotein (MEVTPSGTWL), triggering memory CD8-positive T cell response (PubMed:18991276, PubMed:32887977). Displays self-peptides sharing a signature motif, namely a Glu at position 2 and a Leu anchor residue at the C-terminus (PubMed:18991276).<ref>PMID:18991276</ref> <ref>PMID:32887977</ref> Allele B41:01: Displays self-peptides sharing a signature motif, namely a Glu at position 2 and Ala or Pro anchor residues at the C-terminus.<ref>PMID:18991276</ref> Allele B44:02: Presents immunodominant viral epitopes derived from EBV/HHV-4 EBNA4 (VEITPYKPTW) and EBNA6 (AEGGVGWRHW, EENLLDFVRF), triggering memory CD8-positive T cell response (PubMed:9620674, PubMed:18991276). Displays self-peptides sharing a signature motif, namely a Glu at position 2 and Phe, Tyr or Trp anchor residues at the C-terminus (PubMed:18991276).<ref>PMID:18991276</ref> <ref>PMID:9620674</ref> Allele B45:01: Displays self-peptides sharing a signature motif, namely a Glu at position 2 and Ala or Pro anchor residues at the C-terminus.<ref>PMID:18991276</ref> Allele B46:01: Preferentially presents nonameric peptides sharing a signature motif, namely Ala and Leu at position 2 and Tyr, Phe, Leu, or Met anchor residues at the C-terminus. The peptide-bound form interacts with KIR2DL3 and inhibits NK cell cytotoxic response in a peptide-specific way.<ref>PMID:28514659</ref> Allele B47:01: Displays self-peptides sharing a signature motif, namely an Asp at position 2 and Leu or Met anchor residues at the C-terminus.<ref>PMID:18991276</ref> Allele B49:01: Displays self-peptides sharing a signature motif, namely a Glu at position 2 and Ile or Val anchor residues at the C-terminus.<ref>PMID:18991276</ref> Allele B50:01: Displays self-peptides sharing a signature motif, namely a Glu at position 2 and Ala or Pro anchor residues at the C-terminus.<ref>PMID:18991276</ref> Allele B51:01: Presents an octomeric HIV-1 epitope derived from gag-pol (TAFTIPSI) to the public TRAV17/TRBV7-3 TCR clonotype, strongly suppressing HIV-1 replication.<ref>PMID:24600035</ref> Allele B54:01: Displays peptides sharing a common signature motif, namely a Pro residue at position 2 and Ala anchor residue at the C-terminus.<ref>PMID:7743181</ref> Allele B55:01: Displays peptides sharing a common signature motif, namely a Pro residue at position 2 and Ala anchor residue at the C-terminus.<ref>PMID:7743181</ref> Allele B56:01: Displays peptides sharing a common signature motif, namely a Pro residue at position 2 and Ala anchor residue at the C-terminus.<ref>PMID:7743181</ref> Allele B57:01: The peptide-bound form recognizes KIR3DL1 and inhibits NK cell cytotoxic response.<ref>PMID:22020283</ref> <ref>PMID:25480565</ref> Allele B67:01: Displays peptides sharing a common signature motif, namely a Pro residue at position 2 and Leu anchor residue at the C-terminus.<ref>PMID:7743181</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human]]	+	[[Category: Homo sapiens]]
		+	[[Category: Human herpesvirus 5 strain Towne]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chabrol, E]]	+	[[Category: Chabrol E]]
-	[[Category: Gras, S]]	+	[[Category: Gras S]]
-	[[Category: Rossjohn, J]]	+	[[Category: Rossjohn J]]
-	~~[[Category: Hla b*3501]]~~	+
-	~~[[Category: Human cmv]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: T cell]]~~	+
-	~~[[Category: Tcr~~]]	+

OCA at 09:59, 16 September 2020

OCA — Wed, 16 Sep 2020 09:59:11 GMT

←Older revision		Revision as of 09:59, 16 September 2020
Line 1:		Line 1:

	==Crystal Structure of HLA B*3501-IPS in complex with a Delta-Beta TCR, clone 12 TCR==		==Crystal Structure of HLA B*3501-IPS in complex with a Delta-Beta TCR, clone 12 TCR==
-	<StructureSection load='4qrr' size='340' side='right' caption='[[4qrr]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='4qrr' size='340' side='right'caption='[[4qrr]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qrr]] is a 5 chain structure with sequence from ~~[http://en.wikipedia.org/wiki/ ] and~~ [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QRR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QRR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qrr]] is a 5 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=4QRR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4QRR FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qrp\|4qrp]], [[4qrq\|4qrq]], [[4qrs\|4qrs]], [[4qrt\|4qrt]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qrp\|4qrp]], [[4qrq\|4qrq]], [[4qrs\|4qrs]], [[4qrt\|4qrt]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HLA-B, HLAB ([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, HLAB ([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=4qrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qrr OCA], [http://pdbe.org/4qrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qrr RCSB], [http://www.ebi.ac.uk/pdbsum/4qrr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qrr ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4qrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qrr OCA], [http://pdbe.org/4qrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qrr RCSB], [http://www.ebi.ac.uk/pdbsum/4qrr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qrr ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 23:		Line 23:

	==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 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Chabrol, E]]		[[Category: Chabrol, E]]
	[[Category: Gras, S]]		[[Category: Gras, S]]
	[[Category: Rossjohn, J]]		[[Category: Rossjohn, J]]
	[[Category: Hla b*3501]]		[[Category: Hla b*3501]]
-	[[Category: ~~Huamn~~ cmv]]	+	[[Category: Human cmv]]
	[[Category: Immune system]]		[[Category: Immune system]]
	[[Category: T cell]]		[[Category: T cell]]
	[[Category: Tcr]]		[[Category: Tcr]]

OCA at 14:04, 11 April 2018

OCA — Wed, 11 Apr 2018 14:04:01 GMT

←Older revision		Revision as of 14:04, 11 April 2018
Line 3:		Line 3:
	<StructureSection load='4qrr' size='340' side='right' caption='[[4qrr]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4qrr' size='340' side='right' caption='[[4qrr]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qrr]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QRR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qrr]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QRR FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qrp\|4qrp]], [[4qrq\|4qrq]], [[4qrs\|4qrs]], [[4qrt\|4qrt]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qrp\|4qrp]], [[4qrq\|4qrq]], [[4qrs\|4qrs]], [[4qrt\|4qrt]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HLA-B, HLAB ([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=4qrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qrr OCA], [http://pdbe.org/4qrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qrr RCSB], [http://www.ebi.ac.uk/pdbsum/4qrr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qrr 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=4qrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qrr OCA], [http://pdbe.org/4qrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qrr RCSB], [http://www.ebi.ac.uk/pdbsum/4qrr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qrr ProSAT]</span></td></tr>
	</table>		</table>
Line 27:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Chabrol, E]]		[[Category: Chabrol, E]]
	[[Category: Gras, S]]		[[Category: Gras, S]]

OCA at 04:30, 5 August 2016

OCA — Fri, 05 Aug 2016 04:30:46 GMT

←Older revision		Revision as of 04:30, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of HLA B*3501-IPS in complex with a Delta-Beta TCR, clone 12 TCR==		==Crystal Structure of HLA B*3501-IPS in complex with a Delta-Beta TCR, clone 12 TCR==
	<StructureSection load='4qrr' size='340' side='right' caption='[[4qrr]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4qrr' size='340' side='right' caption='[[4qrr]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4qrr]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QRR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qrr]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QRR FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qrp\|4qrp]], [[4qrq\|4qrq]], [[4qrs\|4qrs]], [[4qrt\|4qrt]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qrp\|4qrp]], [[4qrq\|4qrq]], [[4qrs\|4qrs]], [[4qrt\|4qrt]]</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=4qrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qrr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qrr RCSB], [http://www.ebi.ac.uk/pdbsum/4qrr 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=4qrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qrr OCA], [http://pdbe.org/4qrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qrr RCSB], [http://www.ebi.ac.uk/pdbsum/4qrr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qrr ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 18:		Line 19:
	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 4qrr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin\|Beta-2 microglobulin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:24, 17 December 2014

OCA — Wed, 17 Dec 2014 10:24:34 GMT

←Older revision		Revision as of 10:24, 17 December 2014
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/1B35_HUMAN 1B35_HUMAN]] Involved in the presentation of foreign antigens to the immune system. [[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. [[http://www.uniprot.org/uniprot/PP65_HCMVT PP65_HCMVT]] Forms part of the matrix of the HCMV virion.		[[http://www.uniprot.org/uniprot/1B35_HUMAN 1B35_HUMAN]] Involved in the presentation of foreign antigens to the immune system. [[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. [[http://www.uniprot.org/uniprot/PP65_HCMVT PP65_HCMVT]] Forms part of the matrix of the HCMV virion.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	alphabeta and gammadelta T cells are disparate T cell lineages that can respond to distinct antigens (Ags) via the use of the alphabeta and gammadelta T cell Ag receptors (TCRs), respectively. Here we characterize a population of human T cells, which we term delta/alphabeta T cells, expressing TCRs comprised of a TCR-delta variable gene (Vdelta1) fused to joining alpha and constant alpha domains, paired with an array of TCR-beta chains. We demonstrate that these cells, which represent approximately 50% of all Vdelta1(+) human T cells, can recognize peptide- and lipid-based Ags presented by human leukocyte antigen (HLA) and CD1d, respectively. Similar to type I natural killer T (NKT) cells, CD1d-lipid Ag-reactive delta/alphabeta T cells recognized alpha-galactosylceramide (alpha-GalCer); however, their fine specificity for other lipid Ags presented by CD1d, such as alpha-glucosylceramide, was distinct from type I NKT cells. Thus, delta/alphabetaTCRs contribute new patterns of Ag specificity to the human immune system. Furthermore, we provide the molecular bases of how delta/alphabetaTCRs bind to their targets, with the Vdelta1-encoded region providing a major contribution to delta/alphabetaTCR binding. Our findings highlight how components from alphabeta and gammadeltaTCR gene loci can recombine to confer Ag specificity, thus expanding our understanding of T cell biology and TCR diversity.
		+
		+	The molecular bases of delta/alphabeta T cell-mediated antigen recognition.,Pellicci DG, Uldrich AP, Le Nours J, Ross F, Chabrol E, Eckle SB, de Boer R, Lim RT, McPherson K, Besra G, Howell AR, Moretta L, McCluskey J, Heemskerk MH, Gras S, Rossjohn J, Godfrey DI J Exp Med. 2014 Dec 15;211(13):2599-615. doi: 10.1084/jem.20141764. Epub 2014 Dec, 1. PMID:25452463<ref>PMID:25452463</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:23, 10 December 2014

OCA — Wed, 10 Dec 2014 16:23:52 GMT

←Older revision		Revision as of 16:23, 10 December 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal Structure of HLA B*3501-IPS in complex with a Delta-Beta TCR, clone 12 TCR==
-		+	<StructureSection load='4qrr' size='340' side='right' caption='[[4qrr]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~The entry~~ 4qrr is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4qrr]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QRR FirstGlance]. <br>
-	~~Authors~~: ~~Gras~~, S., ~~Chabrol~~, E., ~~Rossjohn~~, J.	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qrp\|4qrp]], [[4qrq\|4qrq]], [[4qrs\|4qrs]], [[4qrt\|4qrt]]</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=4qrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qrr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qrr RCSB], [http://www.ebi.ac.uk/pdbsum/4qrr PDBsum]</span></td></tr>
-	~~Description~~: ~~Crystal Structure~~ of ~~HLA B*3501~~-~~IPS~~ in ~~complex with a Delta~~-~~Beta TCR~~, ~~clone 12 TCR~~	+	</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/1B35_HUMAN 1B35_HUMAN]] Involved in the presentation of foreign antigens to the immune system. [[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. [[http://www.uniprot.org/uniprot/PP65_HCMVT PP65_HCMVT]] Forms part of the matrix of the HCMV virion.
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chabrol, E]]
		+	[[Category: Gras, S]]
		+	[[Category: Rossjohn, J]]
		+	[[Category: Hla b*3501]]
		+	[[Category: Huamn cmv]]
		+	[[Category: Immune system]]
		+	[[Category: T cell]]
		+	[[Category: Tcr]]

OCA at 06:38, 26 November 2014

OCA — Wed, 26 Nov 2014 06:38:29 GMT

←Older revision		Revision as of 06:38, 26 November 2014
Line 5:		Line 5:
	Authors: Gras, S., Chabrol, E., Rossjohn, J.		Authors: Gras, S., Chabrol, E., Rossjohn, J.

-	Description:	+	Description: Crystal Structure of HLA B*3501-IPS in complex with a Delta-Beta TCR, clone 12 TCR

OCA at 08:15, 24 September 2014

OCA — Wed, 24 Sep 2014 08:15:04 GMT

←Older revision		Revision as of 08:15, 24 September 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4qrr is ON HOLD	+	The entry 4qrr is ON HOLD until Paper Publication

	Authors: Gras, S., Chabrol, E., Rossjohn, J.		Authors: Gras, S., Chabrol, E., Rossjohn, J.

	Description:		Description:

OCA: Protected "4qrr" [edit=sysop:move=sysop]

OCA — Wed, 09 Jul 2014 06:53:25 GMT

Protected "4qrr" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:53, 9 July 2014