Reconstruction of DNA-directed RNA polymerase complex. (a) The RNA Polymerase II-TFIIS complex (PDB ID 1y1v) with 13 subunits (from chain A to chain S). Every chain is one protein (shown by their UniProtKB accessions) and their complex interactions form the large polymer. (b) The PfamA domain architecture for every protein. (c) The cooperative domains identified by our method with protein interaction pairs containing them. The red or blue colors of proteins and domains indicate their memberships.