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. 2008 Apr;64(Pt 4):454-65.
doi: 10.1107/S0907444908003351. Epub 2008 Mar 19.

Multiple crystal structures of actin dimers and their implications for interactions in the actin filament

Michael R Sawaya  1 , D S Kudryashov, Inna Pashkov, Helty Adisetiyo, Emil Reisler, Todd O Yeates
Affiliations

Multiple crystal structures of actin dimers and their implications for interactions in the actin filament

Michael R Sawaya et al. Acta Crystallogr D Biol Crystallogr. 2008 Apr.

Abstract

The structure of actin in its monomeric form is known at high resolution, while the structure of filamentous F-actin is only understood at considerably lower resolution. Knowing precisely how the monomers of actin fit together would lead to a deeper understanding of the dynamic behavior of the actin filament. Here, a series of crystal structures of actin dimers are reported which were prepared by cross-linking in either the longitudinal or the lateral direction in the filament state. Laterally cross-linked dimers, comprised of monomers belonging to different protofilaments, are found to adopt configurations in crystals that are not related to the native structure of filamentous actin. In contrast, multiple structures of longitudinal dimers consistently reveal the same interface between monomers within a single protofilament. The reappearance of the same longitudinal interface in multiple crystal structures adds weight to arguments that the interface visualized is similar to that in actin filaments. Highly conserved atomic interactions involving residues 199-205 and 287-291 are highlighted.

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Figures

Figure 1
Figure 1
Crystal structures of laterally cross-linked actin dimers showing subunit rearrangements that are not consistent with the arrangements of actin monomers in the F-actin filament. (a) A structure of the lateral dimer complexed with KabC determined in space group P212121 (see Table 1 ▶). (b) A second structure of the lateral dimer complexed with KabC, also in space group P212121 but with different unit-cell parameters to (a). It was found to be isomorphous to a previously reported structure of monomeric actin (PDB code 1qz5; Klenchin et al., 2003 ▶). (c) A third lateral interaction (also cross-linked by pPDM) reported in an actin trimer (Dawson et al., 2003 ▶). (d) A lateral pair of actin monomers from the Holmes model of the F-actin filament (Holmes et al., 1990 ▶) shown for reference. Two actin monomers are shown, each colored according to the actin subdomains (subdomains 1, 2, 3 and 4 are colored blue, yellow, red and green, respectively).
Figure 2
Figure 2
New crystal structure of the longitudinally cross-linked actin dimer and a comparison to previously reported arrangements of actin molecules. (a) Eight models showing similar arrangements of longitudinally related actin monomers. The actin subdomains are colored as in Fig. 1 ▶. The models are labeled A–H as in Tables 3 ▶ and 4 ▶. Where present, the bound nucleotide is shown in black. (b) Stereoview showing the protein backbones of the eight models of the longitudinal interface. The lower monomers have been superimposed. Subdomain 4 of the lower monomer is shown in green. Subdomain 3 of the upper monomer is shown in red for the six crystal structures and in purple and pink for the two filament models G and H, respectively. (c) The degree of variation between the different instances of the longitudinal actin interface, based on a principal component analysis. The atomic positions analyzed are those of the atoms in the bottom region of the upper monomer after the lower monomers had been superimposed. The plotted positions of the various models give an indication of the r.m.s. deviation between them (see Table 4 ▶).
Figure 3
Figure 3
Contact maps highlighting the regions of interaction in the various instances of the longitudinal actin interface visualized in crystal structures and filament models. Interfaces from eight different models are shown, labeled A–H as in Tables 3 ▶ and 4 ▶. Regions of close contact are shown in red. Residues belonging to the top region of the lower monomer are indicated along the left side of each map, while residues belonging to the bottom region of the top monomer are indicated along the top. The six models from crystal structures (A–F) show especially strong similarities. The color map shown divides the range of contact distances between 4 and 12 Å into 11 bins, with a uniform spacing in the squared distance.
Figure 4
Figure 4
A stereoview of some of the conserved atomic interactions in the longitudinal actin interface. Interfaces from the six independent crystal structures are shown. Shown in red are three structures (models A, B and D) that group together in the lower left quadrant of the principal component analysis plot (Fig. 2 ▶ c). Shown in blue are two structures (C and E) that fall in the lower right quadrant of the principal component analysis plot. Shown in green is the single crystal structure (F) that appears in the upper right quadrant of the principal component analysis plot. Highlighted interactions include the frequently observed hydrogen bond between Thr203 and Asp288.
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