Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor Mutant

Structure. 2016 Oct 4;24(10):1719-1728. doi: 10.1016/j.str.2016.06.026. Epub 2016 Sep 8.


The immune checkpoint receptor PD-1 and its ligand, PD-L1, have emerged as key regulators of anti-tumor immunity in humans. Recently, we reported an ultra-high-affinity PD-1 mutant, termed high-affinity consensus (HAC) PD-1, which shows superior therapeutic efficacy in mice compared with antibodies. However, the molecular details underlying the action of this agent remain incompletely understood, and a molecular view of PD-1/PD-L1 interactions in general is only beginning to emerge. Here, we report the structure of HAC PD-1 in complex with PD-L1, showing that it binds PD-L1 using a unique set of polar interactions. Biophysical studies and long-timescale molecular dynamics experiments reveal the mechanisms by which ten point mutations confer a 35,000-fold enhancement in binding affinity, and offer atomic-scale views of the role of conformational dynamics in PD-1/PD-L1 interactions. Finally, we show that the HAC PD-1 exhibits pH-dependent affinity, with pseudo-irreversible binding in a low pH setting akin to the tumor microenvironment.

MeSH terms

  • B7-H1 Antigen / chemistry*
  • B7-H1 Antigen / metabolism*
  • Binding Sites
  • Crystallography, X-Ray
  • Humans
  • Hydrogen-Ion Concentration
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Point Mutation*
  • Programmed Cell Death 1 Receptor / chemistry
  • Programmed Cell Death 1 Receptor / genetics
  • Programmed Cell Death 1 Receptor / metabolism*
  • Protein Binding
  • Protein Structure, Secondary


  • B7-H1 Antigen
  • CD274 protein, human
  • PDCD1 protein, human
  • Programmed Cell Death 1 Receptor