Structure of the 34 kDa F-actin-bundling protein ABP34 from Dictyostelium discoideum

The crystal structure of the 34 kDa F‐actin‐bundling protein ABP34 from Dictyostelium discoideum was solved by Ca2+/S‐SAD phasing and refined at 1.89 Å resolution. ABP34 is a calcium‐regulated actin‐binding protein that cross‐links actin filaments into bundles. Its in vitro F‐actin‐binding and F‐actin‐bundling activities were confirmed by a co‐sedimentation assay and transmission electron microscopy. The co‐localization of ABP34 with actin in cells was also verified. ABP34 adopts a two‐domain structure with an EF‐hand‐containing N‐domain and an actin‐binding C‐domain, but has no reported overall structural homologues. The EF‐hand is occupied by a calcium ion with a pentagonal bipyramidal coordination as in the canonical EF‐hand. The C‐domain structure resembles a three‐helical bundle and superposes well onto the rod‐shaped helical structures of some cytoskeletal proteins. Residues 216–244 in the C‐domain form part of the strongest actin‐binding sites (193–254) and exhibit a conserved sequence with the actin‐binding region of α‐actinin and ABP120. Furthermore, the second helical region of the C‐domain is kinked by a proline break, offering a convex surface towards the solvent area which is implicated in actin binding. The F‐actin‐binding model suggests that ABP34 binds to the side of the actin filament and residues 216–244 fit into a pocket between actin subdomains −1 and −2 through hydrophobic interactions. These studies provide insights into the calcium coordination in the EF‐hand and F‐actin‐binding site in the C‐domain of ABP34, which are associated through interdomain interactions.