Polyomavirus origins of replication contain multiple occurrences of G(A/G)GGC, the high-affinity binding element for the viral initiator T-antigen (T-ag).The site I regulatory region of simian virus 40, involved in the repression of transcription and the enhancement of DNA replication initiation, contains two GAGGC sequences arranged head to tail and separated by a 7-bp AT-rich sequence. We have solved a 3.2-Å costructure of the SV40 origin-binding domain (OBD) bound to site I. We have also established that T-ag assembly on site I is limited to the formation of a single hexamer. These observations have enabled an analysis of the role(s) of the OBDs bound to the site I pentanucleotides in hexamer formation. Of interest, they reveal a correlation between the OBDs bound to site I and a pair of OBD subunits in the previously described hexameric spiral structure. Based on these findings, we propose that spiral assembly is promoted by pentanucleotide pairs arranged in a head-to-tail manner. Finally, the possibility that spiral assembly by OBD subunits accounts for the heterogeneous distribution of pentanucleotides found in the origins of replication of polyomaviruses is discussed. P olyomaviruses are small DNA tumor viruses implicated in human diseases, particularly among the immunocompromised and the elderly (1). For example, the polyomavirus JC causes progressive multifocal leukoencephalopathy (PML) (2), BK virus is correlated with renal dysfunction in kidney transplant patients (2), and Merkel cell polyomavirus (MCV) is implicated in a rare but aggressive form of skin cancer (3, 4). The recent identification of several new human polyomaviruses (e.g., KI and WU polyomaviruses [5]) have provided additional incentives to establish fundamental aspects of the polyomavirus life cycle.The best-studied member of the polyomavirus family is simian virus 40 (SV40). Advances made with SV40 include the identification of several of the tumor suppressor proteins targeted during viral transformation (reviewed in reference 6). It has also been used to identify many of the proteins required for eukaryotic DNA replication (reviewed in references 7 to 9). In related studies, it was used to establish basic mechanisms involved in the replication process (reviewed in references 10 to 12). A current focus of research in this field is providing a molecular understanding of initiation events (reviewed in reference 13). In the long term, it is anticipated that progress made in terms of understanding SV40 replication will lead to therapies for treating polyomavirus infections.Among the highly conserved features of the circular, doublestranded DNA genomes of polyomavirus family members are the origins of DNA replication. The minimal or "core" origin of SV40 is a 64-bp region that is necessary and sufficient for DNA replication (reference 14 and references therein) (Fig. 1A). The central region of the core origin (termed site II) contains a palindromic arrangement of four GAGGC pentanucleotides (termed P1 to P4). The pentanucleotides are the hi...