(a) The atomic model of the quaternary RFC–3′-DNA1–5′-DNA2–PCNA complex. The Rfc1 BRCT domain caps 5′-DNA2. Regions in the two blue boxes are enlarged in (c) and (d). (b) Structure of the yeast Rfc1 BRCT domain in the context of the full RFC complex bound to DNA (DNA not shown) compared with the human RFC1 BRCT domain (aa 375–480; PDB entry 2K7F). The human RFC1 BRCT was computationally modeled to recognize the 5′-junction of dsDNA by the end region of β1–2. (c) Enlarged view showing interactions between RFC and 3′-DNA1. Helices α4 and α5 of the AAA-ATP domain of Rfc1, 4, 3 and 2 wrap around the template strand. DNA is shown as stubs with the separated base pair (dA-12:dT-19) and base dA-20 in primer strand shown in sticks. Residues Arg-632 and Gln-636 (from Rfc1), Lys-275 (from Rfc4) contacting the bases of DNA are in salmon sticks. Residues H-bonding with DNAs are in yellow. The main chain nitrogen atoms of Ile-86, Ile-90, and Ile-103 in the α4 helices of Rfc4, 3 and 2 form H-bonds with template DNA. (d) Enlarged view of the 5′-DNA2 binding region. The positively charged Rfc1 BRCT domain on top and positively charged AAA+ module from the bottom stabilize the 5′-DNA2. Key residues surrounding 5′-DNA2 are labelled. The α-helix of Rfc1 collar domain harboring Phe-552 and His-556 (cyan sticks) blocks the 5′-DNA2 5′-junction. The “separation pin” residue Phe-666 located at the DNA2 5′-junction, Arg-476 and Arg-663 (salmon sticks) insert into the DNA minor groove, while Arg-477 (yellow stick) point to the DNA major groove. For clarity, only partial protein secondary structures are shown. Unless noted otherwise, the same color and rendering scheme is used in all figures. (e) The arrangement of 3′-DNA1 and 5′-DNA2 in RFC (left) resembles a gapped DNA (right).