Figure 6
From: Structure-function analysis of the DNA-binding domain of a transmembrane transcriptional activator
HADDOCK model of the CadC1-107 structure with the Cad1 17-mer DNA. (a) Overlay of all 26 ensemble structures within the respective cluster from a HADDOCK modelling of CadC1-107 with Cad1 17-mer DNA (Supplementary Table S3). (b) Alignment of the lowest-energy model for the CadC1-107/Cad1 DNA complex from (a) with the structure of the PhoB-pho box DNA complex (PDB: 1gxp16) (see Fig. 1d). DNAs are coloured according to proteins. (c) Superposition of a SAXS-derived ab initio shape model of a 1:1 complex of CadC1-107 with 17-mer Cad1 DNA (grey, semi-transparent) with the lowest-energy structure from the cluster in (a) shown as blue cartoon. (d) Contacts of CadC1-107 in complex with Cad1 17-mer DNA. Red lines indicate sequence-specific interactions of protein side chains with DNA bases. Black lines are contacts to the DNA backbone, i.e. the phosphate or the sugar groups. Green lines show relevant, sequence-specific protein-protein contacts.
