Figure 6

PCNA-DNA contacts in the X-ray derived PCNA-DNA model. (A) Electrostatic surface representation of the center of PCNA; positive electrostatic surfaces are colored blue, negative surfaces are red, and neutral surfaces are white. Note the interactions made between the negatively charged backbone of DNA strand 1 (depicted as spheres) and the positively charged patch located in the center of PCNA formed by residues Lys 13, Arg 14, Lys 146, and Arg 149. The PCNA subunit in the foreground is removed for clarity. (B) Contacts between DNA and the His 190 loop and Asn 84 loops are indicated. (C) The PCNA-DNA model and an adjacent PCNA molecule in the crystal lattice (the adjacent PCNA molecule is rendered as a surface). The DNA end protruding from the distal face of the clamp forms a crystal contact. (D) Close-up view of the positions of the DNA molecules from the RFC-PCNA-DNA model and the PCNA-DNA model relative to PCNA. The angles of the DNA molecules in the RFC-PCNA-DNA model and the PCNA-DNA model differ by ~26°. Note the positions of residues identified to interact with DNA from the RFC ATPase assay and the PCNA-DNA model. DNA phosphates are shown as spheres. A PCNA subunit is removed from the foreground for clarity. (E) Overlay of PCNA-DNA model and β clamp-DNA structure [25], aligned on their respective clamps. The β clamp is removed for clarity. On the right, the angles of the two DNA molecules are compared relative to the rotation axis of the clamp to which they are bound.