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Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex

Cellular & Molecular Immunology volume 17, pages 966–975 (2020)Cite this article

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Abstract

Leukocyte immunoglobulin (Ig)-like receptors (LILRs), also known as CD85 and immunoglobulin-like transcripts (ILTs), play pivotal roles in regulating immune responses. These receptors define an immune checkpoint that immune therapy can target. Through cis or trans interactions with human leukocyte antigen (HLA)-G, the two most abundantly expressed inhibitory LILRs, LILRB1, and LILRB2 (LILRB1/2, also known as CD85j/d and ILT2/4), are involved in immunotolerance in pregnancy and transplantation, autoimmune diseases, and immune evasion by tumors. Although the discrete domains of LILRB1/2 are clear, the assembly mode of the four extracellular Ig-like domains (D1, D2, D3, and D4) remains unknown. Previous data indicate that D1D2 is responsible for binding to HLA class I (HLA-I), but the roles of D3D4 are still unclear. Here, we determined the crystal structure of the four Ig-like domain LILRB2 and four-domain LILRB1 in complex with HLA-G1. The angles between adjacent domains and the staggered assembly of the four domains suggest limited flexibility and limited plasticity of the receptors during ligand binding. The complex structure of four-domain LILRB1 and HLA-G1 supports the model that D1D2 is responsible for HLA-I binding, while D3D4 acts as a scaffold. Accordingly, cis and trans binding models for HLA-I binding to LILRB1/2 are proposed. The geometries of LILRB1/2 in complex with dimeric and monomeric HLA-G1 suggest the accessibility of the dimeric receptor, which in turn, transduces more inhibitory signals. The assembly of LILRB1/2 and its binding to HLA-G1 could aid in the design of immune regulators and benefit immune interference.

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Data availability

The accession numbers for the atomic coordinates and diffraction data reported in this paper are PDB 6AED (crystal structure of LILRB2) and 6AEE (crystal structure of LILRB1/HLA-G1 complex), respectively.

References

  1. Brown, D., Trowsdale, J. & Allen, R. The LILR family: modulators of innate and adaptive immune pathways in health and disease. Tissue Antigens. 64, 215–225 (2004).

    Article  CAS  Google Scholar 

  2. Takeda, K. & Nakamura, A. Regulation of immune and neural function via leukocyte Ig-like receptors. J. Biochem. 162, 73–80 (2017).

    Article  CAS  Google Scholar 

  3. Zhang, J. et al. Leukocyte immunoglobulin-like receptors in human diseases: an overview of their distribution, function, and potential application for immunotherapies. J. Leukoc. Biol. 102, 351–360 (2017).

    Article  CAS  Google Scholar 

  4. Colonna, M. et al. A common inhibitory receptor for major histocompatibility complex class I molecules on human lymphoid and myelomonocytic cells. J. Exp. Med. 186, 1809–1818 (1997).

    Article  CAS  Google Scholar 

  5. Shiroishi, M. et al. Human inhibitory receptors Ig-like transcript 2 (ILT2) and ILT4 compete with CD8 for MHC class I binding and bind preferentially to HLA-G. Proc. Natl Acad. Sci. USA 100, 8856–8861 (2003).

    Article  CAS  Google Scholar 

  6. Merlo, A. et al. Inhibitory receptors CD85j, LAIR-1, and CD152 down-regulate immunoglobulin and cytokine production by human B lymphocytes. Clin. Diagn. Lab. Immunol. 12, 705–712 (2005).

    Article  CAS  Google Scholar 

  7. Favier, B., LeMaoult, J., Lesport, E. & Carosella, E. D. ILT2/HLA-G interaction impairs NK-cell functions through the inhibition of the late but not the early events of the NK-cell activating synapse. FASEB J. 24, 689–699 (2010).

    Article  CAS  Google Scholar 

  8. Ponte, M. et al. Inhibitory receptors sensing HLA-G1 molecules in pregnancy: decidua-associated natural killer cells express LIR-1 and CD94/NKG2A and acquire p49, an HLA-G1-specific receptor. Proc. Natl Acad. Sci. USA. 96, 5674–5679 (1999).

    Article  CAS  Google Scholar 

  9. Masuda, A., Nakamura, A., Maeda, T., Sakamoto, Y. & Takai, T. Cis binding between inhibitory receptors and MHC class I can regulate mast cell activation. J. Exp. Med. 204, 907–920 (2007).

    Article  CAS  Google Scholar 

  10. Mori, Y. et al. Inhibitory immunoglobulin-like receptors LILRB and PIR-B negatively regulate osteoclast development. J. Immunol. 181, 4742–4751 (2008).

    Article  CAS  Google Scholar 

  11. Roberti, M. P. et al. Overexpression of CD85j in TNBC patients inhibits Cetuximab-mediated NK-cell ADCC but can be restored with CD85j functional blockade. Eur. J. Immunol. 45, 1560–1569 (2015).

    Article  CAS  Google Scholar 

  12. Barkal, A. A. et al. Engagement of MHC class I by the inhibitory receptor LILRB1 suppresses macrophages and is a target of cancer immunotherapy. 19, 76–84 Nat. Immunol. (2017).

  13. Kang, X. et al. Inhibitory leukocyte immunoglobulin-like receptors: Immune checkpoint proteins and tumor sustaining factors. Cell Cycle. 15, 25–40 (2016).

    Article  CAS  Google Scholar 

  14. Willcox, B. E., Thomas, L. M. & Bjorkman, P. J. Crystal structure of HLA-A2 bound to LIR-1, a host and viral major histocompatibility complex receptor. Nat. Immunol. 4, 913–919 (2003).

    Article  CAS  Google Scholar 

  15. Shiroishi, M. et al. Structural basis for recognition of the nonclassical MHC molecule HLA-G by the leukocyte Ig-like receptor B2 (LILRB2/LIR2/ILT4/CD85d). Proc. Natl Acad. Sci. USA. 103, 16412–16417 (2006).

    Article  CAS  Google Scholar 

  16. Yang, Z. & Bjorkman, P. J. Structure of UL18, a peptide-binding viral MHC mimic, bound to a host inhibitory receptor. Proc. Natl Acad. Sci. USA. 105, 10095–10100 (2008).

    Article  Google Scholar 

  17. Dulberger, C. L. et al. Human leukocyte antigen F presents peptides and regulates immunity through interactions with NK cell receptors. Immunity. 46, 1018–1029 e1017 (2017).

    Article  CAS  Google Scholar 

  18. Mohammed, F. et al. The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status. Oncotarget. 8, 54160–54172 (2017).

    Article  Google Scholar 

  19. Chapman, T. L., Heikeman, A. P. & Bjorkman, P. J. The inhibitory receptor LIR-1 uses a common binding interaction to recognize class I MHC molecules and the viral homolog UL18. Immunity. 11, 603–613 (1999).

    Article  CAS  Google Scholar 

  20. Huang, J. et al. HLA-B*35-Px-mediated acceleration of HIV-1 infection by increased inhibitory immunoregulatory impulses. J. Exp. Med. 206, 2959–2966 (2009).

    Article  CAS  Google Scholar 

  21. Gao, X. et al. Effect of a single amino acid change in MHC class I molecules on the rate of progression to AIDS. N. Engl. J. Med. 344, 1668–1675 (2001).

    Article  CAS  Google Scholar 

  22. Steinle, A. et al. Motif of HLA-B*3503 peptide ligands. Immunogenetics. 43, 105–107 (1996).

    Article  CAS  Google Scholar 

  23. Lichterfeld, M. 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).

    Article  CAS  Google Scholar 

  24. Yang, Y., Huang, J., Toth, I., Lichterfeld, M. & Yu, X. G. Mutational escape in HIV-1 CTL epitopes leads to increased binding to inhibitory myelomonocytic MHC class I receptors. PLoS ONE. 5, e15084 (2010).

    Article  CAS  Google Scholar 

  25. Nam, G. et al. Crystal structures of the two membrane-proximal Ig-like domains (D3D4) of LILRB1/B2: alternative models for their involvement in peptide-HLA binding. Protein Cell. 4, 761–770 (2013).

    Article  CAS  Google Scholar 

  26. Lichterfeld, M. & Yu, X. G. The emerging role of leukocyte immunoglobulin-like receptors (LILRs) in HIV-1 infection. J. Leukoc. Biol. 91, 27–33 (2012).

    Article  CAS  Google Scholar 

  27. Chapman, T. L., Heikema, A. P., West, A. P. & Bjorkman, P. J. Crystal structure and ligand binding properties of the D1D2 region of the inhibitory receptor LIR-1 (ILT2). Immunity. 13, 727–736 (2000).

  28. Willcox, B. E. et al. Crystal structure of LIR-2 (ILT4) at 1.8 Å: differences from LIR-1 (ILT2) in regions implicated in the binding of the human cytomegalovirus class I MHC homolog UL18. BMC Struct. Biol. 2, 6 (2002).

    Article  Google Scholar 

  29. Shiroishi, M. et al. Efficient leukocyte Ig-like receptor signaling and crystal structure of disulfide-linked HLA-G dimer. J. Biol. Chem. 281, 10439–10447 (2006).

    Article  CAS  Google Scholar 

  30. Colonna, M. et al. A common inhibitory receptor for major histocompatibility complex class I molecules on human lymphoid and myelomonocytic cells. J. Exp. Med. 186, 1809–1818 (1997).

    Article  CAS  Google Scholar 

  31. Chen, Y. et al. Crystal structure of myeloid cell activating receptor leukocyte Ig-like receptor A2 (LILRA2/ILT1/LIR-7) domain swapped dimer: molecular basis for its non-binding to MHC complexes. J. Mol. Biol. 386, 841–853 (2009).

    Article  CAS  Google Scholar 

  32. Cheng, H. et al. Crystal structure of leukocyte Ig-like receptor LILRB4 (ILT3/LIR-5/CD85k): a myeloid inhibitory receptor involved in immune tolerance. J. Biol. Chem. 286, 18013–18025 (2011).

    Article  CAS  Google Scholar 

  33. Zhang, W. et al. Crystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA) reveals similar antigenicity to that of the 1918 pandemic virus. Protein Cell. 1, 459–467 (2010).

    Article  CAS  Google Scholar 

  34. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  37. Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank the staff of BL17U beamline at SSRF. We are grateful to Zheng Fan from the Institute of Microbiology Chinese Academy of Sciences (CAS) for technical assistance with the SPR experiments. This work was supported by the Strategic Priority Research Program of CAS (grant no. XDA12020358), the National Basic Research Program (973) of China (grant no. 2015CB910503), and the National Natural Science Foundation of China (NSFC, grant nos 31502078 and 31390432). Q.W. is supported by the Youth Innovation Promotion Association CAS (grant no. 2018119). H.S. is supported by the Young Elite Scientist Sponsorship Program by CAST (2016QNRC001) and the Youth Innovation Promotion Association CAS (2017117). G.F.G. is a leading principal investigator of the NSFC Innovative Research Group (Grant no. 81621091).

Author contributions

Y.S. and G.F.G. initiated and coordinated the project. Q.W., H.S., Y.S., J.Y. and G.F.G. designed the experiments. Q.W. and H.S. conducted the experiments with the assistance of G.N. Q.W. obtained diffractable complex crystals of LILRB1 and HLA-G1, and H.S. obtained diffractable crystals of free LILRB2. J.Q. solved the crystal structures. Q.W., H.S., H.C., Y.S., J.Y. and G.F.G. analyzed the data. Q.W. wrote the manuscript. H.S., S.T., J.W., M.F., Z.T., X.C., Z.A., J.Y. and G.F.G revised the manuscript.

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  1. These authors contributed equally: Qihui Wang, Hao Song

Authors and Affiliations

  1. CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China

    Qihui Wang & Jinghua Yan

  2. Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 77030, Houston, TX, USA

    Qihui Wang & Zhiqiang An

  3. Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China

    Hao Song, Hao Cheng & George F. Gao

  4. CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China

    Jianxun Qi, Gol Nam, Shuguang Tan, Min Fang, Yi Shi, Jinghua Yan & George F. Gao

  5. Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, 100050, Beijing, China

    Junzhi Wang

  6. Savaid Medical School, University of Chinese Academy of Sciences, 101408, Beijing, China

    Yi Shi & George F. Gao

  7. Institute of Immunology and CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, 230027, Hefei, China

    Zhigang Tian

  8. National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, 200433, Shanghai, China

    Xuetao Cao

  9. Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, 100005, Beijing, China

    Xuetao Cao

  10. College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China

    Jinghua Yan

  11. Collaborative Innovation Center for diagnosis and treatment of infectious diseases, Zhejiang University, 310003, Hangzhou, China

    George F. Gao

  12. National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), 102206, Beijing, China

    George F. Gao

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  1. Qihui Wang
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Correspondence to Qihui Wang or George F. Gao.

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Wang, Q., Song, H., Cheng, H. et al. Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex. Cell Mol Immunol 17, 966–975 (2020). https://doi.org/10.1038/s41423-019-0258-5

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