Figure 5.

PLD3 and PLD4 form homodimers

(A) Size exclusion chromatography (SEC) run of PLD3 superimposed with the SEC run of PLD4.

(B) Mass distribution of PLD3 and PLD4 observed by mass photometry.

(C) Ribbon representation of the PLD3 dimer shown together with the cryo-EM density map. The inset shows a detailed view of the dimer interface, with the involved residues shown in stick representations. The mutated residue R340 and active site HxK motifs are highlighted in pink.

(D) Structural comparison between the PLD3 cryo-EM structure, colored in turquoise and dark blue, and the PLD4 model predicted by Alphafold, colored in beige. The inset illustrates the comparison of the PLD3/PLD4 dimer interface, with involved residues highlighted using stick representations.

(E) Representative 2D classes of PLD4 particles illustrating the dimeric conformation.

(F) Size exclusion chromatography (SEC) run of PLD3 superimposed with the SEC run of PLD3(R340D). Note that the SEC control run of PLD3 is identical to Figure 5A.

(G) Mass distribution of PLD3 and PLD3(R340D) observed by mass photometry. Note that the mass distribution control of PLD3 is identical to Figure 5B.

(H and I) Urea gels of RNA9.2s^O and CpG^O-DNA digested with indicated concentrations of PLD3 and PLD3(R340D). One out of two independent experiments is shown.