Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling

Chromatin remodeling factors assume critical roles by regulating access to nucleosomal DNA. To determine the architecture of the Drosophila ISWI remodeling enzyme, we developed an integrative structural approach that combines protein cross-linking, mass spectrometry, small-angle X-ray scattering, and computational modeling. The resulting structural model shows the ATPase module in a resting state with both ATPase lobes twisted against each other, providing support for a conformation that was recently trapped by crystallography. The autoinhibiting NegC region does not protrude from the ATPase module as suggested previously. The regulatory NTR domain is located near both ATPase lobes. The full-length enzyme is flexible and can adopt a compact structure in solution with the C-terminal HSS domain packing against the ATPase module. Our data imply a series of conformational changes upon activation of the enzyme and illustrate how the NTR, NegC, and HSS domains contribute to regulation of the ATPase module. [Display omitted] •Full-length DmISWI structure revealed by XL-MS, SAXS, and computational modeling•The two ATPase lobes are captured in a resting state in solution•The flanking NTR and HSS domains pack against the ATPase core•Large conformational changes are predicted upon binding to the nucleosome Harrer et al. reconstruct the conformation of the full-length ISWI chromatin remodeling enzyme in solution using an integrative structural approach. The model captures ISWI in the resting state and implies dramatic conformational changes upon binding to its nucleosome substrate.