AlphaFold predictions and NEDD1 conservation analysis. (A) Cartoon representation of AlphaFold 3 prediction of four copies each of human NEDD1(571–660), MZT1, and GCP3(1–120) colored by subunit (left) and pLDDT (right). (B) Partial alignment error plot for the prediction in A. (C) Cartoon representation of AlphaFold 3 prediction of four copies each of human NEDD1(571–660), MZT2A, and GCP2(1–120) colored by subunit (left) and pLDDT (right). (D) Partial alignment error plot for the prediction in C. (E) Cartoon representation of AlphaFold 3 prediction of full-length A. thaliana NEDD1, MZT1A, and GCP3 colored by subunit (left) and pLDDT (right). (F) Partial alignment error plot for the prediction in E. (G) Cartoon representation of AlphaFold 3 prediction of full-length A. thaliana NEDD1, MZT1A, and GCP5A colored by subunit (left) and pLDDT (right). (H) Partial alignment error plot for the prediction in G. Yellow boxes in F and H highlight expected regions for the formation of NEDD1:MZT:GCP–NHD subcomplexes. (I) Cartoon representation of AlphaFold 3 model of the NEDD1 pinwheel in A. MZT1 and GCP3-NHD are colored according to the legend in A; NEDD1 is colored according to conservation as scored in the color key. A multiple sequence alignment of 141 annotated protein sequences across various species was used to score conservation. Residues mutated in this study are shown in stick representation on the right-hand model of NEDD1 alone. (J) Conservation of NEDD1 residues 571–660. Generated using WebLogo (Crooks et al., 2004).