Abstract

Major histocompatibility complex class I (MHC-I) molecules play a crucial role in immunity by capturing peptides for presentation to T cells and natural killer (NK) cells. The peptide termini are tethered within the MHC-I antigen-binding groove, but it is unknown whether other presentation modes occur. Here we show that 20% of the HLA-B*57:01 peptide repertoire comprises N-terminally extended sets characterized by a common motif at position 1 (P1) to P2. Structures of HLA-B*57:01 presenting N-terminally extended peptides, including the immunodominant HIV-1 Gag epitope TW10 (TSTLQEQIGW), showed that the N terminus protrudes from the peptide-binding groove. The common escape mutant TSNLQEQIGW bound HLA-B*57:01 canonically, adopting a dramatically different conformation than the TW10 peptide. This affected recognition by killer cell immunoglobulin-like receptor (KIR) 3DL1 expressed on NK cells. We thus define a previously uncharacterized feature of the human leukocyte antigen class I (HLA-I) immunopeptidome that has implications for viral immune escape. We further suggest that recognition of the HLA-B*57:01-TW10 epitope is governed by a 'molecular tension' between the adaptive and innate immune systems.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Referenced accessions

Protein Data Bank

References

  1. 1.

    , & Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 Å resolution. J. Mol. Biol. 219, 277–319 (1991).

  2. 2.

    , & MHC ligands and peptide motifs: first listing. Immunogenetics 41, 178–228 (1995).

  3. 3.

    , , , & MHC/peptide binding studies indicate hierarchy of anchor residues. Cell. Immunol. 151, 158–167 (1993).

  4. 4.

    & Structural analysis of MHC class I molecules with bound peptide antigens. Semin. Immunol. 5, 75–80 (1993).

  5. 5.

    , , , & Specificity pockets for the side chains of peptide antigens in HLA-Aw68. Nature 342, 692–696 (1989).

  6. 6.

    , , , & Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa. Immunity 14, 81–92 (2001).

  7. 7.

    et al. High resolution structures of highly bulged viral epitopes bound to major histocompatibility complex class I. Implications for T-cell receptor engagement and T-cell immunodominance. J. Biol. Chem. 280, 23900–23909 (2005).

  8. 8.

    et al. Peptide specificity in the recognition of MHC class I by natural killer cell clones. Science 267, 1016–1018 (1995).

  9. 9.

    , , & Peptide sequence requirements for the recognition of HLA-B*2705 by specific natural killer cells. J. Immunol. 157, 3350–3356 (1996).

  10. 10.

    et al. Crystal structures and KIR3DL1 recognition of three immunodominant viral peptides complexed to HLA-B*2705. Eur. J. Immunol. 35, 341–351 (2005).

  11. 11.

    , & Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1-HLA-Cw4 complex. Nat. Immunol. 2, 452–460 (2001).

  12. 12.

    et al. Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B. Nature 479, 401–405 (2011).

  13. 13.

    , & Three-dimensional structure of a peptide extending from one end of a class I MHC binding site. Nature 371, 626–629 (1994).

  14. 14.

    et al. Antigen processing influences HIV-specific cytotoxic T lymphocyte immunodominance. Nat. Immunol. 10, 636–646 (2009).

  15. 15.

    et al. Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove. eLife 5, e12556 (2016).

  16. 16.

    , , & Longer peptide can be accommodated in the MHC class I binding site by a protrusion mechanism. Eur. J. Immunol. 30, 3089–3099 (2000).

  17. 17.

    , , , & A comprehensive analysis of constitutive naturally processed and presented HLA-C*04:01 (Cw4)-specific peptides. Tissue Antigens 83, 174–179 (2014).

  18. 18.

    & The influence of HLA genotype on AIDS. Annu. Rev. Med. 54, 535–551 (2003).

  19. 19.

    et al. HLA B*5701 is highly associated with restriction of virus replication in a subgroup of HIV-infected long term nonprogressors. Proc. Natl. Acad. Sci. USA 97, 2709–2714 (2000).

  20. 20.

    et al. AIDS restriction HLA allotypes target distinct intervals of HIV-1 pathogenesis. Nat. Med. 11, 1290–1292 (2005).

  21. 21.

    et al. Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nat. Med. 2, 405–411 (1996).

  22. 22.

    et al. Association between presence of HLA-B*5701, HLA-DR7, and HLA-DQ3 and hypersensitivity to HIV-1 reverse-transcriptase inhibitor abacavir. Lancet 359, 727–732 (2002).

  23. 23.

    et al. Immune self-reactivity triggered by drug-modified HLA-peptide repertoire. Nature 486, 554–558 (2012).

  24. 24.

    et al. Genetic variations in HLA-B region and hypersensitivity reactions to abacavir. Lancet 359, 1121–1122 (2002).

  25. 25.

    et al. Novel, cross-restricted, conserved, and immunodominant cytotoxic T lymphocyte epitopes in slow progressors in HIV type 1 infection. AIDS Res. Hum. Retroviruses 12, 1691–1698 (1996).

  26. 26.

    et al. Characterization of HLA-B57-restricted human immunodeficiency virus type 1 Gag- and RT-specific cytotoxic T lymphocyte responses. J. Gen. Virol. 79, 2191–2201 (1998).

  27. 27.

    , , & Maintenance of viral suppression in HIV-1-infected HLA-B*57+ elite suppressors despite CTL escape mutations. J. Exp. Med. 203, 1357–1369 (2006).

  28. 28.

    , , , & Human immunodeficiency virus mutations during the first month of infection are preferentially found in known cytotoxic T-lymphocyte epitopes. J. Virol. 79, 11523–11528 (2005).

  29. 29.

    et al. Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection. J. Virol. 85, 10518–10528 (2011).

  30. 30.

    et al. Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. J. Virol. 80, 3617–3623 (2006).

  31. 31.

    et al. Dynamics and timing of in vivo mutations at Gag residue 242 during primary HIV-1 subtype C infection. Virology 403, 37–46 (2010).

  32. 32.

    et al. HLA-B57/B*5801 human immunodeficiency virus type 1 elite controllers select for rare gag variants associated with reduced viral replication capacity and strong cytotoxic T-lymphocyte [corrected] recognition. J. Virol. 83, 2743–2755 (2009).

  33. 33.

    et al. An early HIV mutation within an HLA-B*57-restricted T cell epitope abrogates binding to the killer inhibitory receptor 3DL1. J. Virol. 85, 5415–5422 (2011).

  34. 34.

    et al. Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection. J. Virol. 81, 8346–8351 (2007).

  35. 35.

    et al. Differential natural killer cell-mediated inhibition of HIV-1 replication based on distinct KIR/HLA subtypes. J. Exp. Med. 204, 3027–3036 (2007).

  36. 36.

    et al. Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS. Nat. Genet. 31, 429–434 (2002).

  37. 37.

    et al. KIR/HLA pleiotropism: protection against both HIV and opportunistic infections. PLoS Pathog. 2, e79 (2006).

  38. 38.

    et al. Human leukocyte antigen class I-restricted activation of CD8+ T cells provides the immunogenetic basis of a systemic drug hypersensitivity. Immunity 28, 822–832 (2008).

  39. 39.

    , , , & Improved visualization of protein consensus sequences by iceLogo. Nat. Methods 6, 786–787 (2009).

  40. 40.

    et al. Mutational and structural analysis of KIR3DL1 reveals a lineage-defining allotypic dimorphism that impacts both HLA and peptide sensitivity. J. Immunol. 192, 2875–2884 (2014).

  41. 41.

    et al. Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3. Cell 82, 655–664 (1995).

  42. 42.

    et al. Large scale mass spectrometric profiling of peptides eluted from HLA molecules reveals N-terminal-extended peptide motifs. J. Immunol. 181, 4874–4882 (2008).

  43. 43.

    et al. A long N-terminal-extended nested set of abundant and antigenic major histocompatibility complex class I natural ligands from HIV envelope protein. J. Biol. Chem. 281, 6358–6365 (2006).

  44. 44.

    , & Virus evasion of MHC class I molecule presentation. J. Immunol. 171, 4473–4478 (2003).

  45. 45.

    & Evasion from NK cell-mediated immune responses by HIV-1. Microbes Infect. 14, 904–915 (2012).

  46. 46.

    , , , & Endocytosis of major histocompatibility complex class I molecules is induced by the HIV-1 Nef protein. Nat. Med. 2, 338–342 (1996).

  47. 47.

    , , & HIV-1 tat inhibits the 20 S proteasome and its 11 S regulator-mediated activation. J. Biol. Chem. 272, 8145–8148 (1997).

  48. 48.

    , , , & HIV type 1 abrogates TAP-mediated transport of antigenic peptides presented by MHC class I. Transporter associated with antigen presentation. AIDS Res. Hum. Retroviruses 18, 1319–1325 (2002).

  49. 49.

    et al. Escape from highly effective public CD8+ T-cell clonotypes by HIV. Blood 118, 2138–2149 (2011).

  50. 50.

    et al. A molecular basis for the interplay between T cells, viral mutants, and human leukocyte antigen micropolymorphism. J. Biol. Chem. 289, 16688–16698 (2014).

  51. 51.

    et al. A molecular basis for the control of preimmune escape variants by HIV-specific CD8+ T cells. Immunity 38, 425–436 (2013).

  52. 52.

    et al. Evolution and transmission of stable CTL escape mutations in HIV infection. Nature 412, 334–338 (2001).

  53. 53.

    et al. Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication. J. Virol. 81, 12382–12393 (2007).

  54. 54.

    et al. Evolution of HLA-B*5703 HIV-1 escape mutations in HLA-B*5703-positive individuals and their transmission recipients. J. Exp. Med. 206, 909–921 (2009).

  55. 55.

    & NK cells in HIV-1 infection: evidence for their role in the control of HIV-1 infection. J. Intern. Med. 265, 29–42 (2009).

  56. 56.

    et al. A viral CTL escape mutation leading to immunoglobulin-like transcript 4-mediated functional inhibition of myelomonocytic cells. J. Exp. Med. 204, 2813–2824 (2007).

  57. 57.

    et al. Kinetics of antigen expression and epitope presentation during virus infection. PLoS Pathog. 9, e1003129 (2013).

  58. 58.

    et al. Common HIV-1 peptide variants mediate differential binding of KIR3DL1 to HLA-Bw4 molecules. J. Virol. 85, 5970–5974 (2011).

  59. 59.

    et al. Killer cell immunoglobulin-like receptor 3DL1 polymorphism defines distinct hierarchies of HLA class I recognition. J. Exp. Med. 213, 791–807 (2016).

  60. 60.

    et al. Rapid screening for the detection of HLA-B57 and HLA-B58 in prevention of drug hypersensitivity. Tissue Antigens 78, 11–20 (2011).

  61. 61.

    et al. Constitutive and inflammatory immunopeptidome of pancreatic β-cells. Diabetes 61, 3018–3025 (2012).

  62. 62.

    & The use of post-source decay in matrix-assisted laser desorption/ionisation mass spectrometry to delineate T cell determinants. J. Immunol. Methods 249, 17–31 (2001).

  63. 63.

    et al. The production, purification and crystallization of a soluble heterodimeric form of a highly selected T-cell receptor in its unliganded and liganded state. Acta Crystallogr. D Biol. Crystallogr. 58, 2131–2134 (2002).

  64. 64.

    & A universal algorithm for fast and automated charge state deconvolution of electrospray mass-to-charge ratio spectra. J. Am. Soc. Mass Spectrom. 9, 225–233 (1998).

  65. 65.

    Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).

  66. 66.

    Scaling and assessment of data quality. Acta Crystallogr. D Biol. Crystallogr. 62, 72–82 (2006).

  67. 67.

    Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography No. 26 (1992).

  68. 68.

    et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

  69. 69.

    & Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

  70. 70.

    et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

  71. 71.

    et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).

Download references

Acknowledgements

This work was supported by project grants from the National Health and Medical Research Council of Australia (NH&MRC; APP1063829 to A.W.P., and APP1099814 to J.P.V. and D.A.P.) and the Australian Research Council (ARC; DP150104503 to J.R. and A.W.P.). A.W.P. is an NH&MRC Senior Research Fellow. P.T.I. is an NH&MRC Early Career Fellow. S.H.R. is the recipient of an Australian Postgraduate Award. D.A.P. is supported by a Wellcome Trust Senior Investigator Award. J.R. is supported by an ARC Laureate Fellowship. This work was funded in part by the intramural program of the National Institutes of Health, National Cancer Institute. This research was carried out in part on the MX2 beamline at the Australian Synchrotron, Victoria, Australia. J. Mak (Deakin University, Melbourne, Victoria, Australia) provided the Gag plasmid and generated the antibody used to assay Gag expression in transfectants.

Author information

Author notes

    • Phillip Pymm
    • , Patricia T Illing
    •  & Sri H Ramarathinam

    These authors contributed equally to this work.

    • Anthony W Purcell
    • , Jamie Rossjohn
    •  & Julian P Vivian

    These authors jointly supervised this work.

Affiliations

  1. Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.

    • Phillip Pymm
    • , Patricia T Illing
    • , Sri H Ramarathinam
    • , Victoria A Hughes
    • , Corinne Hitchen
    • , Bosco K Ho
    • , Anthony W Purcell
    • , Jamie Rossjohn
    •  & Julian P Vivian
  2. Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.

    • Phillip Pymm
    • , Victoria A Hughes
    • , Jamie Rossjohn
    •  & Julian P Vivian
  3. Department of Biological Sciences, University of Chester, Chester, UK.

    • Geraldine M O'Connor
  4. Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK.

    • David A Price
    •  & Jamie Rossjohn
  5. Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.

    • David A Price
  6. Cancer and Inflammation Program, National Cancer Institute–Frederick, Frederick, Maryland, USA.

    • Daniel W McVicar
  7. Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia.

    • Andrew G Brooks

Authors

  1. Search for Phillip Pymm in:

  2. Search for Patricia T Illing in:

  3. Search for Sri H Ramarathinam in:

  4. Search for Geraldine M O'Connor in:

  5. Search for Victoria A Hughes in:

  6. Search for Corinne Hitchen in:

  7. Search for David A Price in:

  8. Search for Bosco K Ho in:

  9. Search for Daniel W McVicar in:

  10. Search for Andrew G Brooks in:

  11. Search for Anthony W Purcell in:

  12. Search for Jamie Rossjohn in:

  13. Search for Julian P Vivian in:

Contributions

P.P., P.T.I., S.H.R. and G.M.O'C. collected and analyzed the data and wrote the manuscript with guidance and intellectual input from D.W.M., A.G.B., A.W.P., J.R. and J.P.V. B.K.H. assisted with bioinformatics analysis. V.A.H. assisted with hydrogen deuterium assays. C.H. assisted with cell culture and protein purification. D.A.P. and all other authors contributed to intellectual discussions on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Anthony W Purcell or Jamie Rossjohn or Julian P Vivian.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–2 and Supplementary Note 1

Excel files

  1. 1.

    Supplementary Table 1

    Combined HLA-B*57:01 data set

  2. 2.

    Supplementary Table 2

    Alignment of N-terminally extended peptide sets

  3. 3.

    Supplementary Table 3

    Extended sets containing C-terminal or N- and C-terminal extensions

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nsmb.3381