Figure 2: Structure of the USP/EcR/IR1 DNA nuclear receptor complex.

(a) Stereo representation of the USP/EcR/hsp27 complex. The cryo-EM map is shown in magenta, with the fit of the individually available crystal structures of the DBD/DNA and LBD heterodimers. The DBDs of USP (blue) and EcR (green) are bound below and in front (side-on) of the DNA (drawn in-plane of the image), with the 5′ DNA end of the leading DNA strand on the left. (b) Class averages of the USP/EcR/hsp27 and USP/EcR/hsp27-3′ complexes with the corresponding maps, revealing a density corresponding to the 18 bp DNA extension on the 3′ side. (c–f) Detailed views of the USP/EcR/hsp27 complex regarding the USP and EcR LBDs, the EcR CTE helix and the antagonist and agonist positions of helix H12 in the USP and EcR LBDs, respectively. (g) Scattering curve (blue) computed from the USP/EcR/hsp27 cryo-EM structure, which is in excellent agreement with the experimental X-ray scattering pattern (black) for the whole range of momentum transfer 0.01<Q<0.5 Å⁻¹ (where Q=4π sin(θ)/λ, where 2θ is the scattering angle and λ is the wavelength) with a χ²=1.54, suggesting the same conformation in solution as analysed by SAXS or cryo-EM. (h,i) Ab initio envelope of the USP/EcR/hsp27 complex (light green) calculated with DAMMIF, and comparison with the cryo-EM map. (j) Comparison of the USP/EcR/hsp27 experimental X-ray scattering pattern (black) and calculated scattering curve (blue) of the cryo-EM structure with the scattering curves calculated from the PPAR/RXR-DR1⁸ and HNF4-1α-DR1 crystal structures¹⁰, which differ significantly at small scattering angles, where PPAR/RXR-DR1 is much less compact in solution than in the crystal⁹, whereas the RXR/LXR/DR4 complex¹² is different from PPAR/RXR and more similar to RXR/VDR/DR3 (ref. 11).