Fig. 5: Cryo-EM structure of the NanR-dimer1/(GGTATA)2-repeat DNA complex.
From: Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism
a A 3.9 Å resolution cryo-EM reconstruction of the E. coli NanR-dimer1/DNA hetero-complex. Reconstruction is shown as transparent isosurfaces fitted with the cartoon representation of the hetero-complex structure. b The (GGTATA)2-repeat DNA oligonucleotide used to solve this dataset, where each repeat is highlighted red. c Overlay of the C-terminal effector-binding domain from the crystal structure (beige and blue) and the cryo-EM structure (green and black) closely match each other (RMSD = 2.1 Å). d Density in the cryo-EM reconstruction that is hypothesized to be Zn2+ (red circle). Coordinating histidine residues are shown as sticks. e Overlay of the N-terminal DNA-binding domain and the flexible α4-linking-helices from the crystal structure (blue) and DNA-bound cryo-EM model (green and black). Note the change in direction of the α4-helix between structures. f Overlay of the interaction between the N-terminal DNA-binding domain and DNA for NanR (green, black, and beige) and FadR (orange and blue) [PDB ID: 1HW2]. A sequence alignment of the N-terminal domain for each structure shows that many of the DNA-binding residues in FadR are conserved in NanR. An asterisk indicates fully conserved residues, a colon indicates conservation between residues of strongly similar properties, and a period indicates conservation between residues of weakly similar properties. Residues proposed to interact with the phosphate backbone are highlighted blue, while residues proposed to interact with the DNA base pairs are highlighted in pink. g–i Close up of the N-terminal domain to highlight the difference in DNA binding between monomer A (green) and B (black). Sidechains of putative DNA-binding residues that could be resolved are shown (e.g., Arg73 and Asn89). A red circle highlights where a sidechain could not be resolved in the opposing monomer.
