The purified T-antigen origin binding domain binds site specifically to site II, the central region of the simian virus 40 core origin. However, in the context of full-length T antigen, the origin binding domain interacts poorly with DNA molecules containing just site II. Here we investigate the contributions of additional core origin regions, termed the flanking sequences, to origin recognition and the assembly of T-antigen hexamers and double hexamers. Results from these studies indicate that in addition to site-specific binding of the T-antigen origin binding domain to site II, T-antigen assembly requires non-sequence-specific interactions between a basic finger in the helicase domain and particular flanking sequences. Related studies demonstrate that the assembly of individual hexamers is coupled to the distortions in the proximal flanking sequence. In addition, the point in the double-hexamer assembly process that is regulated by phosphorylation of threonine 124, the sole posttranslational modification required for initiation of DNA replication, was further analyzed. Finally, T-antigen structural information is used to model various stages of T-antigen assembly on the core origin and the regulation of this process.Recent studies have established many of the factors required for initiation of DNA replication in eukaryotic organisms (reviewed in references 3 and 75). However, at the molecular level, this process is still poorly understood. In higher eukaryotic organisms this situation reflects, in part, the failure to identify sequences that define origins of replication (26). As a result, little is known about the protein-DNA interactions that are essential for initiation of replication. A further limitation is that structural information is available for only a few of the proteins involved in initiation of eukaryotic DNA replication.Therefore, basic issues related to initiation of eukaryotic DNA replication have been addressed by using viral model systems. One of the more useful viral model systems for studying DNA replication is simian virus 40 (SV40) (reviewed in references 8, 25, and 61). The SV40 origin of replication is well defined (reviewed in references 5 and 8), as is the viral initiator protein, termed T antigen (T-ag), a 708-amino-acid phosphoprotein containing several domains (8,25,61). Moreover, the interaction of T-ag with the core origin has been extensively studied (reviewed in references 8, 25, and 61). A further advantage afforded by this system is that considerable information about the structure of T-ag has been obtained. For instance, the structure of the T-ag domain that site-specifically binds to the SV40 origin, the origin binding domain (T-ag-obd) (residues 131 to 260), was determined by nuclear magnetic resonance methods (41). In addition, crystallographic techniques were used to determine the structures of the J domaincontaining (11, 67) N terminus of T-ag (residues 7 to 117) (35) and the C-terminal helicase domain (residues 251 to 627) (39). That this structural information is of...