Fig. 1
Alphafold 3 modelling of S. cerevisiae protein Ccw12. (A) The predicted 3D structure of Ccw12. The structure is colour-coded to reflect local confidence scores per amino acid residue (plDDT), with light green indicating low confidence and dark green indicating high confidence. Blue triangles denote N-glycosylated asparagines linked to core glycans. Red triangles mark three conserved cysteine residues, two of which form a disulphide bond. On the right, predicted aligned error (PAE) diagrams for Ccw12 and Ccw22 illustrate global interaction confidence between amino acid residues, with light green denoting low confidence and dark green denoting high confidence. Below the 3D model, the uppermost track outlines the Ccw12 primary sequence, showing the signal sequence, the Pfam domain PF13928 (which folds into a flocculin type 3 repeat), Ccw12-characteristic repeats R1 and R2, and the GPI transamidase-targeted ω-site. The second track correlates these features to their plDDT scores, while the last track indicates sequence similarity to Ccw22, with blue lines marking identical or similar residues. (B) Homodimer formation. Ccw12 can potentially form homodimers, in which two monomers link through the C72-C72 interchain disulphide bond, indicated by the red arrow and accentuated in the ellipsoid inset showing a top-down view of the homodimer. The bottom PAE diagrams show Alphafold 3 predicts the formation of Ccw12 and Ccw22 homo- and heterodimers with similar confidence. (C) Homotrimer formation. Ccw12 might also form homotrimers, in which three C72 residues group together, with two forming an interchain disulphide bond. Such cysteine grouping is highlighted by the red arrow and in the top-down view of the complex in the circular inset. (D) Forming heterodimers with other cell wall proteins. Ccw12 potentially forms heterodimers with other cell wall proteins that carry the 3β-strand motif. The panel shows the PAE diagram between the cell wall proteins Ccw12 and Flo10, with grey triangles highlighting potential protein-protein interactions between the motifs. The circular inset displays aligned 3β-strand motifs from Ccw12 (green) and Flo10 (blue), emphasizing their similarity, while the bottom 3D structure depicts the predicted Ccw12-Flo10 complex