4X3N
Crystal structure of 34 kDa F-actin bundling protein from Dictyostelium discoideum
Summary for 4X3N
| Entry DOI | 10.2210/pdb4x3n/pdb |
| Descriptor | Calcium-regulated actin-bundling protein, CALCIUM ION, CITRIC ACID, ... (4 entities in total) |
| Functional Keywords | actin, cytoskeleton, bundling, protein binding |
| Biological source | Dictyostelium discoideum (Slime mold) |
| Total number of polymer chains | 3 |
| Total formula weight | 100502.88 |
| Authors | Kim, M.-K.,Kim, J.-H.,Kim, J.-S.,Kang, S.-O. (deposition date: 2014-12-01, release date: 2015-09-16, Last modification date: 2024-03-20) |
| Primary citation | Kim, M.K.,Kim, J.H.,Kim, J.S.,Kang, S.O. Structure of the 34 kDa F-actin-bundling protein ABP34 from Dictyostelium discoideum. Acta Crystallogr.,Sect.D, 71:1835-1849, 2015 Cited by PubMed Abstract: The crystal structure of the 34 kDa F-actin-bundling protein ABP34 from Dictyostelium discoideum was solved by Ca(2+)/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. PubMed: 26327373DOI: 10.1107/S139900471501264X PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.89 Å) |
Structure validation
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