Extended Data Fig. 9. Data processing for 30 min time points.

a, 2D classes from the 30 min time point show the presence of the extended HA2 (state IV) and the post-fusion conformations, as well as a minor population of neutral-pH conformations. The post-fusion averages are interpretable only for the end-on view down the threefold axis, where this conformation forms a characteristic dense ring-like shape. This limited range of interpretable views is probably due to the, now flexibly linked, HA1 domains increasing the structural heterogeneity. The interpretability of this species could be improved by the addition of 10 mM of 2-mercaptoethanol to detach the disulfide-linked HA1 domains. b, Classification scheme for the 30-min time point supplemented with 2-mercaptoethanol. c, FSC curve for the final refined structure, with resolution criterion FSC = 0.143 shown.