Fig. 4: The conformation of Arp3 in the branch junction depends on the bound nucleotide.
a–d Electrostatic potential densities, and nucleotide models in the nucleotide pockets of Arp3 and Arp2 with stick diagrams of the catalytic glutamine and histidine. a Arp3 with BeFx showing density for ADP, BeFx and Mg2+. b Arp3 without BeFx has no density for a γ-phosphate. c–d Maps of Arp2 (from ADP-BeFx and ADP states, respectively) have density for ATP including the γ-phosphate and Mg2+. e Ribbon diagram of Arp3 with a bar showing the axis of rotation between the inner and outer domains. The curved arrow indicates the motion of the outer domain when the inner domain is held fixed in space. f–g Comparison of the conformations of Arp3 in the ADP-BeFx (orange opaque) and ADP-bound (orange transparent) structures. Arp3 is flatter with bound BeFx because subdomains 1 (SD1) and 2 (SD2) are rotated ~2° relative to the ADP-bound structure. The rotation axis in e and f was computed with UCSF ChimeraX as follows: two copies of the Arp3 model from our ADP branch structure were fitted by least-squares alignment to the Arp3 model in our ADP-BeFx branch structure. One ADP Arp3 model was fitted by subdomains 3 and 4, while the other was fitted by subdomains 1 and 2. The geometric transformation between the two ADP structures was then obtained by the ‘measure rotation’ command in UCSF ChimeraX. This procedure estimates the rotation axis together with the rotation angle and shift along the axis needed to superimpose subdomains 1 and 2 (which includes the D-loop) while holding subdomains 3 and 4 fixed.
