A comparison of the lowest energy ensemble of structures of the ID3 stem–loop and a cartoon of the ID3–IBS1 complex. Starting with the structure of the ID3–IBS1 complex of Kruschel and Sigel (PDB: 2K64), we modified conformation of the backbone of ID3 to accommodate our NMR data using the modeling features of Pymol (The PyMOL Molecular Graphics System, version 1.2r3pre, Schrödinger) and added two residues 3′ to IBS1 that were used in our studies. Geometry was based on A-form backbone parameters and stacking information from base-base NOEs within the complex. Helical constraints of the EBS1–IBS1 pairing, limited by the length of the ID3 loop, result in a large distance between U8 and A10′ and U9 and G9′, preventing formation of additional base pairs.
