Extended Data Fig. 6: Details of integrated cell montages of CBQ- and DMSO-treated P. falciparum parasites and quantitative proteomic analysis.

a, Integrated cell montage of a CBQ-treated parasite frozen, milled and imaged at 3 h post-treatment. Averaged central slices from tomograms collected on the cell are shown mapped onto a tracing of the cell, with ultrastructural segmentations and mapped back ribosome reconstructions overlaid on top. Segmented features are color coded as indicated by corresponding colored labels. Mapped back ribosomes are colored as follows: orange=monomers, pale-yellow=dimers and polysomes, red=membrane bound ribosomes. b-c, Integrated cell montage of a DMSO-vehicle parasite frozen, milled and imaged at 3 h (b) and 18 h (c) post-treatment. Segmentation is colored as in (a). c, Detailed view of the averaged central slices overlaid with segmentations containing the DV of the cell shown in (a). Segmented features are color coded as in (a). PVM, parasitophorous vacuolar membrane. PPM, parasite plasma membrane. EMS, endomembrane system. DV, digestive vacuole. Hz, hemozoin. ER, endoplasmic reticulum. d, Total count of number of nuclei containing Pf60S at 3 and 18 h under DMSO-vehicle and CBQ-treatment. e, Hema3-stained smears of parasites at 3, 18 and 36 h after addition of CBQ or DMSO- vehicle (23, 38, and 56 hpi). Parasites treated with DMSO-vehicle have egressed and reinvaded by the 36 hr (56 hpi) time point from three biological and technical replicates. f, Volcano plot showing differentially expressed proteins under CBQ-pressure comparing proteins present at 36 h to 3 h post treatment (56 to 23 hpi). The mean average of each protein from three replicates (n = 3) is shown. Y-axes show log10 p- value and x-axes show log₂ fold change using nested study design. Dark coral and blue circles indicate proteins with significant enrichment and depletion, respectively. Grey circles indicate proteins with no significant (p > 0.05) change in expression. Hit selection cut-offs of p < 0.05 and log2 Fold-change of >0.1 are represented by dashed lines. One way ANOVA and pairwise comparison was used to compare each condition.