3vcl

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Crystal Structure of HLA-B7 with the HCMV pp65 peptide RPHERNGFTVL

Structural highlights

3vcl is a 3 chain structure with sequence from Homo sapiens and Human betaherpesvirus 5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

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 B*15:02.^[1] Disease susceptibility is associated with variants affecting the gene represented in this entry. A restricted number of HLA-B*27 subtypes can be associated with ankylosing spondylitis and other B*27-related diseases, and an elevated frequency of the B*27:02 allele in ankylosing spondylitis patients is identified. The allele B*27:07 seems to have a protective role in some populations because it was found only in the healthy controls.^[2] There is evidence that HLA-B*51 is associated with susceptibility to Behcet disease (BD). However, it is not certain whether HLA-B*51 itself or a closely linked gene is responsible for susceptibility. The world distribution of HLA-B*51 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-B*51 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-B*51 would support other nongenetic risk factors.^[3] The presence of allele B*57:01 is associated with increased susceptibility to abacavir hypersensitivity [MIM:142830 in HIV-1 patients.^[4] Allele group B*08 is associated with increased susceptibility to rheumatoid arthritis, where affected individuals have antibodies to cyclic citrullinated peptide (anti-CCP-positive rheumatoid arthritis).^[5]

Function

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).^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] Allele B*07:02: 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).^[13] ^[14] ^[15] ^[16] Allele B*08:01: Presents to CD8-positive T cells viral epitopes derived from EBV/HHV-4 EBNA3 (QAKWRLQTL), eliciting cytotoxic T cell response.^[17] Allele B*13:02: 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.^[18] Allele B*18:01: 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).^[19] ^[20] ^[21] ^[22] Allele B*27:05: 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-B*27:05 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).^[23] ^[24] ^[25] ^[26] ^[27] ^[28] ^[29] Allele B*40:01: 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).^[30] ^[31] Allele B*41:01: Displays self-peptides sharing a signature motif, namely a Glu at position 2 and Ala or Pro anchor residues at the C-terminus.^[32] Allele B*44:02: 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).^[33] ^[34] Allele B*45:01: Displays self-peptides sharing a signature motif, namely a Glu at position 2 and Ala or Pro anchor residues at the C-terminus.^[35] Allele B*46:01: 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.^[36] Allele B*47:01: Displays self-peptides sharing a signature motif, namely an Asp at position 2 and Leu or Met anchor residues at the C-terminus.^[37] Allele B*49:01: Displays self-peptides sharing a signature motif, namely a Glu at position 2 and Ile or Val anchor residues at the C-terminus.^[38] Allele B*50:01: Displays self-peptides sharing a signature motif, namely a Glu at position 2 and Ala or Pro anchor residues at the C-terminus.^[39] Allele B*51:01: Presents an octomeric HIV-1 epitope derived from gag-pol (TAFTIPSI) to the public TRAV17/TRBV7-3 TCR clonotype, strongly suppressing HIV-1 replication.^[40] Allele B*54:01: Displays peptides sharing a common signature motif, namely a Pro residue at position 2 and Ala anchor residue at the C-terminus.^[41] Allele B*55:01: Displays peptides sharing a common signature motif, namely a Pro residue at position 2 and Ala anchor residue at the C-terminus.^[42] Allele B*56:01: Displays peptides sharing a common signature motif, namely a Pro residue at position 2 and Ala anchor residue at the C-terminus.^[43] Allele B*57:01: The peptide-bound form recognizes KIR3DL1 and inhibits NK cell cytotoxic response.^[44] ^[45] Allele B*67:01: Displays peptides sharing a common signature motif, namely a Pro residue at position 2 and Leu anchor residue at the C-terminus.^[46]

Publication Abstract from PubMed

The TCR plays a critical role in recognizing intracellular pathogens and initiating pathways leading to the destruction of infected cells by the immune system. Although genetic variability is known to greatly impact on the human immune system and the outcome of infection, the influence of sequence variation leading to the inactivation or deletion of TCR gene segments is unknown. To investigate this issue, we examined the CD8(+) T cell response to an HLA-B7-restricted epitope ((265)RPHERNGFTVL(275)) from the pp65 Ag of human CMV that was highly biased and frequently dominated by a public TCR beta-chain encoded by the variable gene segment TRBV4-3. Approximately 40% of humans lack T cells expressing TRBV4-3 because of a 21.5-kb insertion/deletion polymorphism, but these individuals remain responsive to this epitope, using a diverse T cell repertoire characterized by private TCR usage. Although most residues within the bulged 11-mer peptide were accessible for TCR contact, the public and private TCRs showed distinct patterns of sensitivity to amino acid substitution at different positions within the peptide, thereby suggesting that the repertoire diversity generated in the absence of the dominant public TRBV4-3(+) TCR could lead to better protection from viral escape mutation. Thus, variation in the size of the TRBV repertoire clearly contributes toward interindividual variability in immune responses and is presumably maintained in many ethnic groups to enhance the diversity of Ag-specific T cell responses.

The impact of a large and frequent deletion in the human TCR beta locus on antiviral immunity.,Brennan RM, Petersen J, Neller MA, Miles JJ, Burrows JM, Smith C, McCluskey J, Khanna R, Rossjohn J, Burrows SR J Immunol. 2012 Mar 15;188(6):2742-8. Epub 2012 Feb 8. PMID:22323539^[47]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

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↑ Varnavidou-Nicolaidou A, Karpasitou K, Georgiou D, Stylianou G, Kokkofitou A, Michalis C, Constantina C, Gregoriadou C, Kyriakides G. HLA-B27 in the Greek Cypriot population: distribution of subtypes in patients with ankylosing spondylitis and other HLA-B27-related diseases. The possible protective role of B*2707. Hum Immunol. 2004 Dec;65(12):1451-4. PMID:15603872 doi:10.1016/j.humimm.2004.08.177
↑ Kirino Y, Bertsias G, Ishigatsubo Y, Mizuki N, Tugal-Tutkun I, Seyahi E, Ozyazgan Y, Sacli FS, Erer B, Inoko H, Emrence Z, Cakar A, Abaci N, Ustek D, Satorius C, Ueda A, Takeno M, Kim Y, Wood GM, Ombrello MJ, Meguro A, Gul A, Remmers EF, Kastner DL. Genome-wide association analysis identifies new susceptibility loci for Behcet's disease and epistasis between HLA-B*51 and ERAP1. Nat Genet. 2013 Feb;45(2):202-7. doi: 10.1038/ng.2520. Epub 2013 Jan 6. PMID:23291587 doi:http://dx.doi.org/10.1038/ng.2520
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↑ Chan KF, Gully BS, Gras S, Beringer DX, Kjer-Nielsen L, Cebon J, McCluskey J, Chen W, Rossjohn J. Divergent T-cell receptor recognition modes of a HLA-I restricted extended tumour-associated peptide. Nat Commun. 2018 Mar 12;9(1):1026. doi: 10.1038/s41467-018-03321-w. PMID:29531227 doi:http://dx.doi.org/10.1038/s41467-018-03321-w
↑ Barber LD, Gillece-Castro B, Percival L, Li X, Clayberger C, Parham P. Overlap in the repertoires of peptides bound in vivo by a group of related class I HLA-B allotypes. Curr Biol. 1995 Feb 1;5(2):179-90. doi: 10.1016/s0960-9822(95)00039-x. PMID:7743181 doi:http://dx.doi.org/10.1016/s0960-9822(95)00039-x
↑ Peh CA, Burrows SR, Barnden M, Khanna R, Cresswell P, Moss DJ, McCluskey J. HLA-B27-restricted antigen presentation in the absence of tapasin reveals polymorphism in mechanisms of HLA class I peptide loading. Immunity. 1998 May;8(5):531-42. doi: 10.1016/s1074-7613(00)80558-0. PMID:9620674 doi:http://dx.doi.org/10.1016/s1074-7613(00)80558-0
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↑ Peng Y, Mentzer AJ, Liu G, Yao X, Yin Z, Dong D, Dejnirattisai W, Rostron T, Supasa P, Liu C, Lopez-Camacho C, Slon-Campos J, Zhao Y, Stuart DI, Paesen GC, Grimes JM, Antson AA, Bayfield OW, Hawkins DEDP, Ker DS, Wang B, Turtle L, Subramaniam K, Thomson P, Zhang P, Dold C, Ratcliff J, Simmonds P, de Silva T, Sopp P, Wellington D, Rajapaksa U, Chen YL, Salio M, Napolitani G, Paes W, Borrow P, Kessler BM, Fry JW, Schwabe NF, Semple MG, Baillie JK, Moore SC, Openshaw PJM, Ansari MA, Dunachie S, Barnes E, Frater J, Kerr G, Goulder P, Lockett T, Levin R, Zhang Y, Jing R, Ho LP, Cornall RJ, Conlon CP, Klenerman P, Screaton GR, Mongkolsapaya J, McMichael A, Knight JC, Ogg G, Dong T. Broad and strong memory CD4(+) and CD8(+) T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat Immunol. 2020 Nov;21(11):1336-1345. doi: 10.1038/s41590-020-0782-6. Epub 2020, Sep 4. PMID:32887977 doi:http://dx.doi.org/10.1038/s41590-020-0782-6
↑ Barber LD, Gillece-Castro B, Percival L, Li X, Clayberger C, Parham P. Overlap in the repertoires of peptides bound in vivo by a group of related class I HLA-B allotypes. Curr Biol. 1995 Feb 1;5(2):179-90. doi: 10.1016/s0960-9822(95)00039-x. PMID:7743181 doi:http://dx.doi.org/10.1016/s0960-9822(95)00039-x
↑ Peh CA, Burrows SR, Barnden M, Khanna R, Cresswell P, Moss DJ, McCluskey J. HLA-B27-restricted antigen presentation in the absence of tapasin reveals polymorphism in mechanisms of HLA class I peptide loading. Immunity. 1998 May;8(5):531-42. doi: 10.1016/s1074-7613(00)80558-0. PMID:9620674 doi:http://dx.doi.org/10.1016/s1074-7613(00)80558-0
↑ Honeyborne I, Prendergast A, Pereyra F, Leslie A, Crawford H, Payne R, Reddy S, Bishop K, Moodley E, Nair K, van der Stok M, McCarthy N, Rousseau CM, Addo M, Mullins JI, Brander C, Kiepiela P, Walker BD, Goulder PJ. Control of human immunodeficiency virus type 1 is associated with HLA-B*13 and targeting of multiple gag-specific CD8+ T-cell epitopes. J Virol. 2007 Apr;81(7):3667-72. doi: 10.1128/JVI.02689-06. Epub 2007 Jan 24. PMID:17251285 doi:http://dx.doi.org/10.1128/JVI.02689-06
↑ Bilsborough J, Panichelli C, Duffour MT, Warnier G, Lurquin C, Schultz ES, Thielemans K, Corthals J, Boon T, van der Bruggen P. A MAGE-3 peptide presented by HLA-B44 is also recognized by cytolytic T lymphocytes on HLA-B18. Tissue Antigens. 2002 Jul;60(1):16-24. doi: 10.1034/j.1399-0039.2002.600103.x. PMID:12366779 doi:http://dx.doi.org/10.1034/j.1399-0039.2002.600103.x
↑ Hickman HD, Luis AD, Buchli R, Few SR, Sathiamurthy M, VanGundy RS, Giberson CF, Hildebrand WH. Toward a definition of self: proteomic evaluation of the class I peptide repertoire. J Immunol. 2004 Mar 1;172(5):2944-52. doi: 10.4049/jimmunol.172.5.2944. PMID:14978097 doi:http://dx.doi.org/10.4049/jimmunol.172.5.2944
↑ Hillen N, Mester G, Lemmel C, Weinzierl AO, Muller M, Wernet D, Hennenlotter J, Stenzl A, Rammensee HG, Stevanovic S. Essential differences in ligand presentation and T cell epitope recognition among HLA molecules of the HLA-B44 supertype. Eur J Immunol. 2008 Nov;38(11):2993-3003. doi: 10.1002/eji.200838632. PMID:18991276 doi:http://dx.doi.org/10.1002/eji.200838632
↑ Rist MJ, Theodossis A, Croft NP, Neller MA, Welland A, Chen Z, Sullivan LC, Burrows JM, Miles JJ, Brennan RM, Gras S, Khanna R, Brooks AG, McCluskey J, Purcell AW, Rossjohn J, Burrows SR. HLA Peptide Length Preferences Control CD8+ T Cell Responses. J Immunol. 2013 Jun 7. PMID:23749632 doi:10.4049/jimmunol.1300292
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↑ Stewart-Jones GB, di Gleria K, Kollnberger S, McMichael AJ, Jones EY, Bowness P. Crystal structures and KIR3DL1 recognition of three immunodominant viral peptides complexed to HLA-B*2705. Eur J Immunol. 2005 Feb;35(2):341-51. PMID:15657948 doi:10.1002/eji.200425724
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↑ Peruzzi M, Wagtmann N, Long EO. A p70 killer cell inhibitory receptor specific for several HLA-B allotypes discriminates among peptides bound to HLA-B*2705. J Exp Med. 1996 Oct 1;184(4):1585-90. doi: 10.1084/jem.184.4.1585. PMID:8879234 doi:http://dx.doi.org/10.1084/jem.184.4.1585
↑ Peh CA, Burrows SR, Barnden M, Khanna R, Cresswell P, Moss DJ, McCluskey J. HLA-B27-restricted antigen presentation in the absence of tapasin reveals polymorphism in mechanisms of HLA class I peptide loading. Immunity. 1998 May;8(5):531-42. doi: 10.1016/s1074-7613(00)80558-0. PMID:9620674 doi:http://dx.doi.org/10.1016/s1074-7613(00)80558-0
↑ Hillen N, Mester G, Lemmel C, Weinzierl AO, Muller M, Wernet D, Hennenlotter J, Stenzl A, Rammensee HG, Stevanovic S. Essential differences in ligand presentation and T cell epitope recognition among HLA molecules of the HLA-B44 supertype. Eur J Immunol. 2008 Nov;38(11):2993-3003. doi: 10.1002/eji.200838632. PMID:18991276 doi:http://dx.doi.org/10.1002/eji.200838632
↑ Peng Y, Mentzer AJ, Liu G, Yao X, Yin Z, Dong D, Dejnirattisai W, Rostron T, Supasa P, Liu C, Lopez-Camacho C, Slon-Campos J, Zhao Y, Stuart DI, Paesen GC, Grimes JM, Antson AA, Bayfield OW, Hawkins DEDP, Ker DS, Wang B, Turtle L, Subramaniam K, Thomson P, Zhang P, Dold C, Ratcliff J, Simmonds P, de Silva T, Sopp P, Wellington D, Rajapaksa U, Chen YL, Salio M, Napolitani G, Paes W, Borrow P, Kessler BM, Fry JW, Schwabe NF, Semple MG, Baillie JK, Moore SC, Openshaw PJM, Ansari MA, Dunachie S, Barnes E, Frater J, Kerr G, Goulder P, Lockett T, Levin R, Zhang Y, Jing R, Ho LP, Cornall RJ, Conlon CP, Klenerman P, Screaton GR, Mongkolsapaya J, McMichael A, Knight JC, Ogg G, Dong T. Broad and strong memory CD4(+) and CD8(+) T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat Immunol. 2020 Nov;21(11):1336-1345. doi: 10.1038/s41590-020-0782-6. Epub 2020, Sep 4. PMID:32887977 doi:http://dx.doi.org/10.1038/s41590-020-0782-6
↑ Hillen N, Mester G, Lemmel C, Weinzierl AO, Muller M, Wernet D, Hennenlotter J, Stenzl A, Rammensee HG, Stevanovic S. Essential differences in ligand presentation and T cell epitope recognition among HLA molecules of the HLA-B44 supertype. Eur J Immunol. 2008 Nov;38(11):2993-3003. doi: 10.1002/eji.200838632. PMID:18991276 doi:http://dx.doi.org/10.1002/eji.200838632
↑ Hillen N, Mester G, Lemmel C, Weinzierl AO, Muller M, Wernet D, Hennenlotter J, Stenzl A, Rammensee HG, Stevanovic S. Essential differences in ligand presentation and T cell epitope recognition among HLA molecules of the HLA-B44 supertype. Eur J Immunol. 2008 Nov;38(11):2993-3003. doi: 10.1002/eji.200838632. PMID:18991276 doi:http://dx.doi.org/10.1002/eji.200838632
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↑ Hillen N, Mester G, Lemmel C, Weinzierl AO, Muller M, Wernet D, Hennenlotter J, Stenzl A, Rammensee HG, Stevanovic S. Essential differences in ligand presentation and T cell epitope recognition among HLA molecules of the HLA-B44 supertype. Eur J Immunol. 2008 Nov;38(11):2993-3003. doi: 10.1002/eji.200838632. PMID:18991276 doi:http://dx.doi.org/10.1002/eji.200838632
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↑ Barber LD, Gillece-Castro B, Percival L, Li X, Clayberger C, Parham P. Overlap in the repertoires of peptides bound in vivo by a group of related class I HLA-B allotypes. Curr Biol. 1995 Feb 1;5(2):179-90. doi: 10.1016/s0960-9822(95)00039-x. PMID:7743181 doi:http://dx.doi.org/10.1016/s0960-9822(95)00039-x
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↑ Barber LD, Gillece-Castro B, Percival L, Li X, Clayberger C, Parham P. Overlap in the repertoires of peptides bound in vivo by a group of related class I HLA-B allotypes. Curr Biol. 1995 Feb 1;5(2):179-90. doi: 10.1016/s0960-9822(95)00039-x. PMID:7743181 doi:http://dx.doi.org/10.1016/s0960-9822(95)00039-x
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