Crystal Structure of the RuvA-RuvB Complex Kazuhiro Yamada, Tomoko Miyata, Daisuke Tsuchiya, Takuji Oyama, Yoshie Fujiwara, Takayuki Ohnishi, Hiroshi Iwasaki, Hideo Shinagawa, Mariko Ariyoshi, Kouta Mayanagi, Kosuke Morikawa  Molecular Cell  Volume 10, Issue 3, Pages 671-681 (September 2002) DOI: 10.1016/S1097-2765(02)00641-X

Figure 1 Interaction between RuvA Domain III and RuvB (A) Gel filtration chromatography of RuvA domain III (red), wild-type RuvB (blue), and the mixture (purple) of domain III-wild-type RuvB. The RuvA domain III fragment spanning residues 129–191 was tested for RuvB binding. The absorbance scale for only domain III is enlarged 10-fold relative to that in the figure. (B) SDS-PAGE of peak fractions of the domain III-RuvB mixture, which forms the 1:1 RuvB-domain III complex. The left two lanes indicate markers for the domain III and RuvB proteins. Molecular Cell 2002 10, 671-681DOI: (10.1016/S1097-2765(02)00641-X)

Figure 2 Structure of the RuvA Domain III-RuvB (1-318) Complex Including AMPPNP (A) Stereo view of a representative difference electron density map (contoured at 2.0 σ) calculated with the composite annealed omit map procedure implemented in CNS (Brünger et al., 1998). The refined model is also displayed in ribbon and stick model representations, with RuvA domain III in yellow and RuvB in magenta. (B) Electron density of AMPPNP and a ribbon model around the nucleotide binding site in the domain III-RuvB complex. The Fo-Fc omit map of AMPPNP is shown at a 2.5 σ contour. Residues interacting with the nucleotide are depicted by their side chains. (C) Stereo view of the overall structure of the domain III-RuvB complex bound to AMPPNP. The ribbon model is viewed from the side of the interface. The domain III and RuvB are colored as shown in (A) and (B). Important residues involved in complex formation are represented by orange (domain III) and blue (RuvB) side chains. (D) Comparison between the domain III-RuvB complex (magenta) and RuvB alone (sky blue) (PDB code; 1HQC). Only Cα backbones of the five parallel β strands of domain N were superimposed between the two structures. The arginine finger (Arg158) of RuvB, which senses the bound nucleotide of an adjacent subunit, is indicated by a blue stick. (E) Contact between domain III and RuvB. The left figure shows RuvA domain III (electrostatic surface representation) bound to RuvB (magenta worm model) mainly through β hairpin 1 of domain N. Likewise, the right figure represents the entire surface of RuvB interacting with domain III (yellow worm model). The views of these figures are rotated by −90° and +90° relative to the model in (C) about the vertical axis, respectively. The positive potential is colored blue and the negative potential is red, as calculated by the GRASP program (Nicholls et al., 1991). The energy scale is from −10.2 kBT to +10.2 kBT for the surface potential. Molecular Cell 2002 10, 671-681DOI: (10.1016/S1097-2765(02)00641-X)

Figure 3 RuvB (1–312, Y309R) Bound to the RuvA Octameric Shell Structure (A) Stereo view of the experimental electron density map around the α9 helix in the RuvB domain C (contoured at 1.0 σ, 3.5 Å resolution), improved with solvent flipping technique. (B) Stereo view of the composite annealed omit map (contoured at 2.0 σ, 3.3 Å resolution) (Brünger et al., 1998) for the same region in (A) which is calculated with the refined atomic coordinates displayed in stick and ribbon model representations. (C) Three orthogonal views showing the overall architecture of the RuvA (yellow)-RuvB (magenta) complex, in which each RuvB subunit binds AMPPNP in an equivalent manner (data not shown). The blue oval indicates the major DNA binding area of domain C. The broken ovals and the lines represent the most probable positions of the disordered domain III and the connecting loop, respectively. (D) Structural similarity between Tth RuvA octamer (yellow) and M. leprae RuvA octamer (blue) highlighted by the superposition of Cα backbones of their core octameric shell structures. The most likely position of domain III (red) in the uncomplexed state is indicated, according to the corresponding position of domain III in the M. leprae RuvA octameric structure (Roe et al., 1998). Molecular Cell 2002 10, 671-681DOI: (10.1016/S1097-2765(02)00641-X)

Figure 4 Averaged Electron Microscopic Image of the RuvA-RuvB-Holliday Junction Ternary Complex and the Corresponding Functional Atomic Model The IMAGIC program package (van Heel et al., 1996) was used to cluster particle images and to obtain class averages. The hypothetical model was constructed by fitting the RuvA octameric core structure (yellow) and the RuvB hexamer models (blue) into the averaged images, referring to the hexameric oligomerization of the HslU protein similar to RuvB (Sousa et al., 2000). One pair of subunits related in each hexameric ring by the central 2-fold axis was replaced by the two domain III (orange)-RuvB (magenta) complexes (see text). Averaged electron microscopic images correspond to two orthogonal views of the ternary complex. The 858 original images were grouped into three major classes of averaged images, and only two of them, (A) and (B), averaged from 171 and 370 electron microscopic images, are shown here. Note the good coincidence of the images with the side (A) and end views (B) of the RuvA octameric core structure. The resolutions of the averaged images of (A) and (B) were estimated at 34 and 31 Å, respectively, from differential phase residuals. The scale bar represents 100 Å. Molecular Cell 2002 10, 671-681DOI: (10.1016/S1097-2765(02)00641-X)

Figure 5 Model of the Loading Process of the RuvA-RuvB Complex on a Holliday Junction Each of the three components in this process was determined by X-ray analyses (forms I, II, and III) or by an electron microscopic study (form IV). The RuvA core region and domain III are colored by yellow and orange, respectively. The RuvB subunit is depicted by a blue oval. Red-trimmed ovals represent domain III bound to the RuvB subunit. The RuvA-RuvB complex (form III) is regarded as the preloading complex before forming the functional complex on a Holliday junction (form IV). During the conversion from form III to IV, the RuvB subunit that was previously connected with the RuvA octameric core is no longer replaced by other partners. Molecular Cell 2002 10, 671-681DOI: (10.1016/S1097-2765(02)00641-X)