The Saccharomyces cerevisiae Mec1 kinase, the mammalian ATR ortholog, is essential for sensing a variety of DNA lesions and initiating DNA damage response. The Dpb11, a homolog of human TopBP1, functions in activating the Mec1 upon DNA replication stress and DNA damages. Here, we report an affinity purification and ion exchange chromatography method to efficiently purify endogenous Dpb11 under normal expression level directly from yeast whole cell extraction. The final concentration of 5 mu M of high purity and homogeneity biochemical preparation enables functional and structural characterization of the physical interaction between Dpb11and Mec1 -Ddc2 complex. The Dpb11 obtained by endogenous purification strongly stimulates the Mecl kinase activity and promotes the changes in conformational distribution. This observation suggests the Dpb11 activates Mec1 kinase probably through modulation in the kinase conformations. (C) 2019 Elsevier Inc. All rights reserved.