Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler

Abstract

The packaging of DNA into nucleosomal structures limits access for templated processes such as transcription and DNA repair. The repositioning or ejection of nucleosomes is therefore critically important for regulated events, including gene expression. This activity is provided by chromatin remodeling complexes, or remodelers, which are typically large, multisubunit complexes that use an ATPase subunit to translocate the DNA. Many remodelers contain pairs or multimers of actin-related proteins (ARPs) that contact the helicase-SANT–associated (HSA) domain within the catalytic ATPase subunit and are thought to regulate ATPase activity. Here, we determined the structure of a four-protein subcomplex within the SWI/SNF remodeler that comprises the Snf2 HSA domain, Arp7, Arp9, and repressor of Ty1 transposition, gene 102 (Rtt102). Surprisingly, unlike characterized actin–actin associations, the two ARPs pack like spoons and straddle the HSA domain, which forms a 92-Å-long helix. The ARP–HSA interactions are reminiscent of contacts between actin and many binding partners and are quite different from those in the Arp2/3 complex. Rtt102 wraps around one side of the complex in a highly extended conformation that contacts both ARPs and therefore stabilizes the complex, yet functions to reduce by ∼2.4-fold the remodeling and ATPase activity of complexes containing the Snf2 ATPase domain. Thus, our structure provides a foundation for developing models of remodeler function, including mechanisms of coupling between ARPs and the ATPase translocation activity.

Crystal structure of a nuclear actin ternary complex

“…2B), which mostly agree with the earlier result, except in the alignment of Snf2 and Ino80 (10). Consistent with a previous suggestion (26), the actin/Apr4 pair is organized in the same way as the Arp7/Arp9 pair, with Arp4 and actin located at the positions of Arp7 and Arp9, respectively ( Fig. 2A).…”

“…1). As suggested (26), the barbed end of N-actin interacts with the amphipathic HSA domain through its hydrophobic cleft. The DNase-Ibinding loop in N-actin subdomain D2, which is suggested to be involved in chromatin binding (25), is disordered.…”

“…Our structure reveals the specific recognition between different HSA helices and the N-actin/ARP pairs. The HSA Snf2 helix is longer than the HSA Swr1 helix, with the N-terminal end binding to the next molecule in the crystal lattice (26). In the structure of the N-actin complex, both the N and C termini of the HSA Swr1 helix are free of crystal packing interactions (Fig.…”

“…The structures of the yeast-specific ARPs, Arp7 and Arp9, when complexed with the HSA domain of the chromatin remodeler Snf2, have been reported (26). To compare these two HSA domain-containing complexes, we aligned the structures of Arp4 and Arp7 ( Fig.…”

Multiple modes of regulation of the human Ino80 SNF2 ATPase by subunits of the INO80 chromatin-remodeling complex

“…Arguing that the HSA module contributes to nucleosome and/or DNA recognition, yeast INO80 complexes lacking the HSA module subunits Arp4, Arp8, and actin neither bind DNA nor support nucleosome remodeling (9), whereas an isolated HSA module composed of the yeast SNF2 HSA domain bound to Arp7, Arp9, and Rtt102 can bind either free or nucleosomal DNA (32). Further, we observed only a partial loss of nucleosome-binding activity in Arp5-and Ies6-deficient complexes purified from cells treated with Ies6 shRNA.…”