Fig. 3: Nucleotide binding to the designed sites, revealed by crystal structures.
a,b, Solved crystal structures viewed from the C-terminal domain of the A subunit and the designed B subunit: A3(De)3 complex structure in the absence of nucleotides (2.8 Å resolution) (a); A3(De)3 complex structure bound to three ADPs in the catalytic interfaces and two ADPs in the designed non-catalytic interfaces (3.2 Å resolution) (b). ADP molecules are shown as spheres. c,d, Superposition of the computational design model of the designed B subunit (white) and the solved crystal structure in the absence of nucleotides (pink) (chain D of A3(De)3_empty was used because this had the highest resolution data of the three designed B subunits): comparison for the entire backbone (the Cα r.m.s.d. calculated by MICAN33 is 1.48 Å) (c); comparison for the designed binding site (d). The backbone geometry of the designed P-loop was almost identical to that of the design model. e, The interface between chains C and D in A3(De)3_(ADP·Pi)1cat(ADP)2cat,2non-cat. The designed P-loop (green) firmly grabs the phosphate group of ADP. The sugar and base of ADP were found at the interface with the A subunit (cyan). The Fo − Fc omit map at 3.0σ obtained by removing ADP and Mg2+ from the model is shown in mesh representation. A stereo view is shown in Supplementary Fig. 8. f,g, Structural comparison for the ATP-binding mode between the computational design model (f) and the solved crystal structure (g) (chain D in A3(De)3_(ADP·Pi)1cat(ADP)2cat,2non-cat). Oxygen, nitrogen and phosphate atoms are coloured red, blue and orange, respectively.
