Chromatin remodelers are ATP-dependent machines that dynamically alter the 
chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing 
nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding 
domain that is required for efficient nucleosome sliding and believed to be 
essential for sensing the length of DNA flanking the nucleosome core. The 
structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT 
and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet 
the details of how Chd1 recognized DNA were not known. Here we present the 
crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in 
complex with a DNA duplex. The bound DNA duplex is straight, consistent with the 
preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. 
Comparison of this structure with the recently solved ISW1a DNA-binding domain 
bound to DNA reveals that DNA lays across each protein at a distinct angle, yet 
contacts similar surfaces on the SANT and SLIDE domains. In contrast to the 
minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of 
the Chd1 DNA-binding domain contacts the DNA major groove. The majority of 
direct contacts with the phosphate backbone occur only on one DNA strand, 
suggesting that Chd1 may not strongly discriminate between major and minor 
grooves.