Fig. 1: Overall structure of the repressor:DNA complex.
a Cartoon representation of the repressor bound to DNA. The protein monomer is colored by domain and includes the N-terminal HTH (residues 15–55, slate blue), the helix bridge (residues 56–74, magenta), and the Stoperator (residues 75–181, orange). The protein secondary structural elements are labeled as either alpha helices (α), beta strands (β), or 310 helices (η), and the two DNA strands are colored in green and white. 2Fo – Fc density, contoured at 1 sigma, is shown in gray for the DNA helix. The two DNA-binding domains engage the DNA via insertion into adjacent openings of the major groove, while the helix bridge serves as a linker between the two DNA-binding domains and lies above the minor groove. b The repressor is shown in surface view and is color-coded as in a. The arrows shown in a, b indicate the direction of transcription. c Surface view of the lambda cI dimer bound to DNA. This image was generated from coordinates 3BDN and shows the two monomers of the cI dimer colored in cyan and brown, with the two DNA strands colored in green and white. In cI, the HTH domain from each monomer of the dimer binds adjacent openings of the major groove. d Superposition of the repressor HTH (slate blue) and the DNA-binding motif of the Stoperator domain (orange). The Stoperator lacks the α2 helix of the HTH domain and also contains a small 310-helix (η1) at its N-terminus. e The region of the Stoperator domain that does not bind the DNA substrate is emphasized with a black circle. An electrostatic surface rendering (red: negative potential, blue: positive potential, white: neutral) reveals that this portion of the protein is acidic in nature.
