Figure 1.

The Asymmetric Unit and Formation of the Functional Unit in the Lattice

(A) Scheme showing the pattern of cleavage of a four-way DNA junction by CtGEN1 and the resulting product formation. Conventionally, we name the four arms B, H, R, and X, and the component strands b, h, r, and x. The arrows show the preferred position of cleavage by CtGEN1, to generate the product (Freeman et al., 2014). This is also shown rotated by 180°to match the view seen in most of the molecular graphics. In the complex CtGEN1 is depicted as a black ellipse, with the active site indicated by the red spot. See also Figure S1B.

(B) Molecular graphics image of the asymmetric unit in the crystal lattice. This comprises a monomer of GEN1 bound to a 14 bp duplex of DNA with a 1 nt 3′ overhang.

(C) Two asymmetric units, showing how each DNA is bound by two GEN1 monomers, colored yellow and blue. See also Movie S1.

(D) F_o-F_c simulated annealing omit map of the electron density at the interface of the two duplexes. This was calculated by omission of the central phosphate of the long strand in the model used to refine the structure. Density corresponding to a phosphate group with partial occupancy is present, clearly linking the two strands. This is consistent with the existence of a 30 nt strand in the crystal. See also Figure S1A.

(E) Parallel-eye stereo molecular graphics image of the functional unit comprising one GEN1 monomer and a product that includes a 30 nt DNA strand. The strands are colored to be consistent with the scheme in (A) with the r strand as the 30 nt strand.