Structure of human upstream binding factor HMG box 5 and site for binding of the cell-cycle regulatory factor TAF1

The fifth HMG-box domain in human upstream binding factor (hUBF) contributes to the synthesis of rRNA by RNA polymerase I (Pol I). The 2.0 Å resolution crystal structure of this protein has been solved using the single-wavelength anomalous dispersion method (SAD). The crystal structure and the reported NMR structure have r.m.s. deviations of 2.18–3.03 Å for the C^α atoms. However, there are significant differences between the two structures, with displacements of up to 9.0 Å. Compared with other HMG-box structures, the r.m.s. deviations for C^α atoms between hUBF HMG box 5 and HMG domains from Drosophila melanogaster protein D and Rattus norvegicus HMG1 are 1.5 and 1.6 Å, respectively. This indicates that the differences between the crystal and NMR structures of hUBF HMG box 5 are larger than those with its homologous structures. The differences between the two structures potentially reflect two states with different structures. The specific interactions between the hUBF HMG box 5 and the first bromodomain of TBP-associated factor 1 (TAF1) were studied by ultrasensitive differential scanning calorimetry and chemical shift perturbation. Based on these experimental data, possible sites in hUBF HMG box 5 that may interact with the first bromodomain of TAF1 were proposed.