Skip to main content
PMC home page
Protein & Cell logoLink to Protein & Cell
. 2010 Feb 6;1(2):153–160. doi: 10.1007/s13238-010-0022-1

A dimeric structure of PD-L1: functional units or evolutionary relics?

Yong Chen 1,2,4, Peipei Liu 1,2, Feng Gao 3, Hao Cheng 1,2, Jianxun Qi 1, George F Gao 1,2,4,5,✉
PMCID: PMC4875164  PMID: 21203985

Abstract

PD-L1 is a member of the B7 protein family, most of whose members so far were identified as dimers in a solution and crystalline state, either complexed or uncomplexed with their ligand(s). The binding of PD-L1 with its receptor PD-1 (CD279) delivers an inhibitory signal regulating the T cell function. Simultaneously with the Garboczi group, we successfully solved another structure of human PD-L1 (hPD-L1). Our protein crystallized in the space group of C2221 with two hPD-L1 molecules per asymmetric unit. After comparison of reported B7 structures, we have found some intrinsic factors involved in the interaction of these two molecules. Based on these results, we tend to believe this uncomplexed hPD-L1 structure demonstrated its potential dimeric state in solution, althougt it could just be an evolutionary relic, too weak to be detected under present technology, or still a functional unit deserved our attentions.

Keywords: PD-L1, crystal structure, dimer, costimulatory molecules, B7 family

Footnotes

These authors contributed equally to the work.

References

  1. Bromley S.K., Iaboni A., Davis S.J., Whitty A., Green J.M., Shaw A.S., Weiss A., Dustin M.L. The immunological synapse and CD28–CD80 interactions. Nat Immunol. 2001;2:1159–1166. doi: 10.1038/ni737. [DOI] [PubMed] [Google Scholar]
  2. CCP4 The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr. 1994;50:760–763. doi: 10.1107/S0907444994003112. [DOI] [PubMed] [Google Scholar]
  3. Chen L.P. Co-inhibitory molecules of the B7–CD28 family in the control of T-cell immunity. Nat Rev Immunol. 2004;4:336–347. doi: 10.1038/nri1349. [DOI] [PubMed] [Google Scholar]
  4. Chen Y., Chu F., Gao F., Zhou B., Gao G.F. Stability engineering, biophysical, and biological characterization of the myeloid activating receptor immunoglobulin-like transcript 1 (ILT1/LIR-7/LILRA2) Protein Expr Purif. 2007;56:253–260. doi: 10.1016/j.pep.2007.08.010. [DOI] [PubMed] [Google Scholar]
  5. Chen Y., Gao F., Chu F., Peng H., Zong L., Liu Y., Tien P., Gao G.F. 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. 2009;386:841–853. doi: 10.1016/j.jmb.2009.01.006. [DOI] [PubMed] [Google Scholar]
  6. Egen J.G., Allison J.P. Cytotoxic T lymphocyte antigen-4 accumulation in the immunological synapse is regulated by TCR signal strength. Immunity. 2002;16:23–35. doi: 10.1016/S1074-7613(01)00259-X. [DOI] [PubMed] [Google Scholar]
  7. Fife B.T., Guleria I., Gubbels Bupp M., Eagar T.N., Tang Q., Bour-Jordan H., Yagita H., Azuma M., Sayegh M.H., Bluestone J. A. Insulin-induced remission in new-onset NOD mice is maintained by the PD-1-PD-L1 pathway. J Exp Med. 2006;203:2737–2747. doi: 10.1084/jem.20061577. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fisicaro P., Boni C., Valdatta C., Bertoletti A., Schivazappa S., Giuberti T., Cavalli A., Missale G., Ferrari C. PD-1/PD-L1 blockade can improve the HBV-specific T cell function in chronic hbv infection. J Hepatol. 2007;46:S56–S56. doi: 10.1016/S0168-8278(07)61723-1. [DOI] [Google Scholar]
  9. Foster C.E., Colonna M., Sun P.D. Crystal structure of the human natural killer (NK) cell activating receptor NKp46 reveals structural relationship to other leukocyte receptor complex immunoreceptors. J Biol Chem. 2003;278:46081–46086. doi: 10.1074/jbc.M308491200. [DOI] [PubMed] [Google Scholar]
  10. Freeman G.J., Long A.J., Iwai Y., Bourque K., Chernova T., Nishimura H., Fitz L.J., Malenkovich N., Okazaki T., Byrne M.C., et al. Engagement of the PD-1 immunoinhibitory receptor by a novel B7 family member leads to negative regulation of lymphocyte activation. J Exp Med. 2000;192:1027–1034. doi: 10.1084/jem.192.7.1027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gao G.F., Gerth U.C., Wyer J.R., Willcox B.E., O’Callaghan C.A., Zhang Z., Jones E.Y., Bell J.I., Jakobsen B.K. Assembly and crystallization of the complex between the human T cell coreceptor CD8alpha homodimer and HLA-A2. Protein Sci. 1998;7:1245–1249. doi: 10.1002/pro.5560070520. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gao G.F., Tormo J., Gerth U.C., Wyer J.R., McMichael A.J., Stuart D.I., Bell J.I., Jones E.Y., Jakobsen B.K. Crystal structure of the complex between human CD8 alpha and HLA-A2. Nature. 1997;387:630–634. doi: 10.1038/42523. [DOI] [PubMed] [Google Scholar]
  13. Greenwald R.J., Freeman G.J., Sharpe A.H. The B7 family revisited. Annu Rev Immunol. 2005;23:515–548. doi: 10.1146/annurev.immunol.23.021704.115611. [DOI] [PubMed] [Google Scholar]
  14. Ikemizu S., Gilbert R.J., Fennelly J.A., Collins A.V., Harlos K., Jones E.Y., Stuart D.I., Davis S.J. Structure and dimerization of a soluble form of B7-1. Immunity. 2000;12:51–60. doi: 10.1016/S1074-7613(00)80158-2. [DOI] [PubMed] [Google Scholar]
  15. Ishida Y., Agata Y., Shibahara K., Honjo T. Induced expression of Pd-1, a novel member of the immunoglobulin gene superfamily, upon programmed cell-death. EMBO J. 1992;11:3887–3895. doi: 10.1002/j.1460-2075.1992.tb05481.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Iwai Y., Ishida M., Tanaka Y., Okazaki T., Honjo T., Minato N. Involvement of PD-L1 on tumor cells in the escape from host immune system and tumor immunotherapy by PD-L1 blockade. Proc Natl Acad Sci U S A. 2002;99:12293–12297. doi: 10.1073/pnas.192461099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Keir M.E., Butte M.J., Freeman G.J., Sharpel A.H. PD-1 and its ligands in tolerance and immunity. Annu Rev Immunol. 2008;26:677–704. doi: 10.1146/annurev.immunol.26.021607.090331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lafferty K.J., Cunningham A.J. A new analysis of allogeneic interactions. Aust J Exp Biol Med. 1975;53:27–42. doi: 10.1038/icb.1975.3. [DOI] [PubMed] [Google Scholar]
  19. Latchman Y.E., Liang S.C., Wu Y., Chernova T., Sobel R.A., Klemm M., Kuchroo V.K., Freeman G.J., Sharpe A.H. PD-L1-deficient mice show that PD-L1 on T cells, antigen-presenting cells, and host tissues negatively regulates Tcells. Proc Natl Acad Sci U S A. 2004;101:10691–10696. doi: 10.1073/pnas.0307252101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lazar-Molnar E., Yan Q., Cao E., Ramagopal U., Nathenson S.G., Almo S.C. Crystal structure of the complex between programmed death-1 (PD-1) and its ligand PD-L2. Proc Natl Acad Sci U S A. 2008;105:10483–10488. doi: 10.1073/pnas.0804453105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lin D.Y., Tanaka Y., Iwasaki M., Gittis A.G., Su H.P., Mikami B., Okazaki T., Honjo T., Minato N., Garboczi D.N. The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors. Proc Natl Acad Sci U S A. 2008;105:3011–3016. doi: 10.1073/pnas.0712278105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lovell S.C., Davis I.W., Arendall W.B., 3rd, de Bakker P.I., Word J. M., Prisant M.G., Richardson J.S., Richardson D.C. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins. 2003;50:437–450. doi: 10.1002/prot.10286. [DOI] [PubMed] [Google Scholar]
  23. McCoy A.J. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr D Biol Crystallogr. 2007;63:32–41. doi: 10.1107/S0907444906045975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Nishimura H., Agata Y., Kawasaki A., Sato M., Imamura S., Minato N., Yagita H., Nakano T., Honjo T. Developmentally regulated expression of the PD-1 protein on the surface of double-negative(CD4-CD8-) thymocytes. Int Immunol. 1996;8:773–780. doi: 10.1093/intimm/8.5.773. [DOI] [PubMed] [Google Scholar]
  25. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997;276:307–326. doi: 10.1016/S0076-6879(97)76066-X. [DOI] [PubMed] [Google Scholar]
  26. Schwartz J.C., Zhang X., Fedorov A.A., Nathenson S.G., Almo S.C. Structural basis for co-stimulation by the human CTLA-4/B7-2 complex. Nature. 2001;410:604–608. doi: 10.1038/35069112. [DOI] [PubMed] [Google Scholar]
  27. Snyder G.A., Brooks A.G., Sun P.D. Crystal structure of the HLA-Cw3 allotype-specific killer cell inhibitory receptor KIR2DL2. Proc Natl Acad Sci U S A. 1999;96:3864–3869. doi: 10.1073/pnas.96.7.3864. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Stamper C.C., Zhang Y., Tobin J.F., Erbe D.V., Ikemizu S., Davis S. J., Stahl M.L., Seehra J., Somers W.S., Mosyak L. Crystal structure of the B7-1/CTLA-4 complex that inhibits human immune responses. Nature. 2001;410:608–611. doi: 10.1038/35069118. [DOI] [PubMed] [Google Scholar]
  29. Trautmann L., Janbazian L., Chomont N., Said E.A., Gimmig S., Bessette B., Boulassel M.R., Delwart E., Sepulveda H., Balderas R.S., et al. Upregulation of PD-1 expression on HIV-specific CD8(+) T cells leads to reversible immune dysfunction. Nat Med. 2006;12:1198–1202. doi: 10.1038/nm1482. [DOI] [PubMed] [Google Scholar]
  30. Urbani S., Amadei B., Tola D., Pedrazzi G., Sacchelli L., Cavallo M.C., Orlandini A., Missale G., Ferrari C. Restoration of HCV-specific T cell functions by PD-1/PD-L1 blockade in HCV infection: Effect of viremia levels and antiviral treatment. J Hepatol. 2008;48:548–558. doi: 10.1016/j.jhep.2007.12.014. [DOI] [PubMed] [Google Scholar]
  31. Willcox B.E., Thomas L.M., Chapman T.L., Heikema A.P., West A. P., Jr., Bjorkman P.J. Crystal structure of LIR-2 (ILT4) at 1.8 A: differences from LIR-1 (ILT2) in regions implicated in the binding of the human cytomegalovirus class I MHC homolog UL18. BMC Struct Biol. 2002;2:6–15. doi: 10.1186/1472-6807-2-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Zhang J.Y., Zhang Z., Wang X., Fu J.L., Yao J., Jiao Y., Chen L., Zhang H., Wei J., Jin L., et al. PD-1 up-regulation is correlated with HIV-specific memory CD8 + T-cell exhaustion in typical progressors but not in long-term nonprogressors. Blood. 2007;109:4671–4678. doi: 10.1182/blood-2006-09-044826. [DOI] [PubMed] [Google Scholar]
  33. Zhang X., Schwartz J.C., Almo S.C., Nathenson S.G. Expression, refolding, purification, molecular characterization, crystallization, and preliminary X-ray analysis of the receptor binding domain of human B7-2. Protein Expr Purif. 2002;25:105–113. doi: 10.1006/prep.2002.1616. [DOI] [PubMed] [Google Scholar]
  34. Zhang X., Schwartz J.C., Almo S.C., Nathenson S.G. Crystal structure of the receptor-binding domain of human B7-2: insights into organization and signaling. Proc Natl Acad Sci U S A. 2003;100:2586–2591. doi: 10.1073/pnas.252771499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Zhu J., Jiang X., Liu Y., Tien P., Gao G.F. Design and characterization of viral polypeptide inhibitors targeting Newcastle disease virus fusion. J Mol Biol. 2005;354:601–613. doi: 10.1016/j.jmb.2005.08.078. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Protein & Cell are provided here courtesy of Oxford University Press

RESOURCES