Nucleolar phosphoprotein 140 (Nopp140) is a nucleolar protein, more than 80% of which is disordered. Previous studies have shown that the C-terminal region of Nopp140 (residues 568-596) interacts with protein kinase CK2 alpha, and inhibits the catalytic activity of CK2. Although the region of Nopp140 responsible for the interaction with CK2 alpha was identified, the structural features and the effect of this interaction on the structure of Nopp140 have not been defined due to the difficulty of structural characterization of disordered protein. In this study, the disordered feature of Nopp140 and the effect of CK2 alpha on the structure of Nopp140 were examined using single-molecule fluorescence resonance energy transfer (smFRET) and electron paramagnetic resonance (EPR). The interaction with CK2 alpha was increased conformational rigidity of the CK2 alpha-interacting region of Nopp140 (Nopp140C), suggesting that the disordered and flexible conformation of Nopp140C became more rigid conformation as it binds to CK2 alpha. In addition, site specific spin labeling and EPR analysis confirmed that the residues 574-589 of Nopp140 are critical for binding to CK2 alpha. Similar technical approaches can be applied to analyze the conformational changes in other IDPs during their interactions with binding partners. (C) 2016 Elsevier Inc. All rights reserved.