Fig. 2: SCAF4_LS binding at the interface between SCAF4 and RNAP2.

a Molecular simulation of SCAF4_LS binding to SCAF4 protein. The colors of SCAF4_LS are color-coded based on the time interval from 400 ns to 500 ns. b Trajectory plot showing the RSMF of five nucleotides over the 400–500 ns time scale. Source data are provided as a Source Data file. c Trajectory plot showing the RSMD of five nucleotides over the 400–500 ns time scale. Source data are provided as a Source Data file. d Overlay of SCAF4_LS sequence and RNAP2 on the surface of SCAF4 protein. Conformations of SCAF4_LS are represented in green cartoon, while RNAP2 peptide is depicted in sand-colored mesh. e Fluorescence polarization measurements where 50 nM FAM-labeled SCAF4_LS was titrated with increasing amounts of SCAF4 mutants. All experiments are performed with three biological replicates, each containing three technical replicates. Affinities of each biological replicate are indicated in the bracket (biological replicates n = 3, mean ± SD). The non-linear fit model and the one-site specific binding to fluorescent population ratio are used for these calculations. Source data are provided as a Source Data file. f Schematic diagram of SCAF4_LS with deletion of base groups at each position. g SPR results showing binding of wild type and base group-deleted SCAF4_LS to SCAF4. Average affinities are generated from three biological replicates, with affinities of each experiment indicated in the bracket (biological replicates n = 3, mean ± SD). Source data are provided as a Source Data file.