Extended Data Fig. 6. The EPYC1_106-135 peptide binds to Rubisco small subunit α-helices via salt bridges and a hydrophobic pocket in a similar manner to the EPYC1_49-72 peptide.

a, The EPYC1_106-135 peptide represents the second, third and fourth Rubisco-binding regions of EPYC1 indicated by pink lines and dash line (the peptide is a perfect match to the second and fourth Rubisco-binding regions, and there is a one-amino acid difference between the peptide and the third repeat). b-c, Side view (b) and top view (c) of the density map of the EPYC1_106-135 peptide-Rubisco complex. Dashes in panel b indicate regions shown in panels d-i. d-e, Front (d) and side (e) views of the EPYC1_106-135 peptide (red) bound to the two α-helices of the Rubisco small subunit (blue). f-g, Three pairs of residues form salt bridges between the helix of the EPYC1_106-135 peptide and the helices on the Rubisco small subunit. Shown are front (f) and side (g) views as in panel d and panel e. The distances from EPYC1 K127, R134 and E129 to Rubisco small subunit E24, D23 and R91 are 2.96 Å, 3.17 Å, and 2.68 Å, respectively. h-i, A hydrophobic pocket is formed by three residues of the EPYC1_106-135 peptide and three residues of helix B of the Rubisco small subunit. Shown are front (h) and side (i) views as in panel d and panel e. j, Summary of the interactions observed between the EPYC1_106-135 peptide and the two α-helices of the Rubisco small subunit. Helices are highlighted; the residues mediating interactions are bold; salt bridges are shown as dotted lines; residues contributing to the hydrophobic pocket are shown in black. k, Color keys used in this figure.