Fig. 1: ERAP1 adopts an open conformation in solution and closes when bound to the substrate and substrate-mimic inhibitors.
a Representative ERAP1 SAXS curve collected using SAXS/WAXS data collection. Data are for ERAP1 reference sequence (isoform I) in the absence of inhibitor or substrate (n = 1 sample was assessed in an independent experiment). Error bars represent uncertainty in log intensity values from radial averaging of scattering profiles. Inset, Guinier plot showing Rg determination using a linear fit of low-resolution scattering data (n = 1, q < 0.04 Å−1); fit value for slope and associated uncertainty are shown. b DG013 induces closed ERAP1 conformation as measured by Rg. Each data point represents an independent experiment (n = 1) processed individually, with the error of linear fit for each dataset shown as error bars. Model for open and closed conformations are based on previously determined ERAP1 crystal structures (2YD0 and 3MDJ chain B) shown for reference are right, with calculated Rg values indicated with dotted vertical lines. An unpaired two-tailed t test was used to assess the significance of the difference between SAXS/WAXS Rg values for ERAP1 in the presence or absence of DG013 from two independent experiments. c ERAP1 experimental SAXS curve (n = 1) from panel a overlaid with calculated SAXS curves generated from three structural models. A largely open model derived from molecular dynamics simulation with q = 67° fits best. Fit residuals for these three models are shown below. d DG013 induces closed ERAP1 conformation as measured by SAXS curve fitting to structural models from molecular dynamics. Models that fit experimental SAXS data with χ2 < 1 are shown as points on the graph from an independent experiment, forming a distribution of models that each fit scattering data within experimental uncertainty. An unpaired two-tailed t test was used to assess significance. Selected ERAP1 models from MD simulation that demonstrate the relationship between angle theta and structural conformation are shown below and on the right is an overlay of selected MD models showing the hinge-like motion of domain IV. e DG013 binds to ERAP1 active site. Polder map (gray mesh) contoured at 3.5 σ shows DG013 electron density at ERAP1 active site. f DG013-bound ERAP1 crystal structure is in the closed conformation. Shown are cartoon and surface representations colored by domain as indicated. Surface cutaway reveals DG013 bound at the active site. Source data are provided as a Source Data file.
