Duck hepatitis B virus (DHBV) shares many fundamental features with human HBV. However, the DHBV core protein (DHBc), forming the nucleocapsid shell, is much larger than that of HBV (HBc) and, in contrast to HBc, there is little direct information on its structure. Here we applied an efficient expression system for recombinant DHBc particles to the biochemical analysis of a large panel of mutant DHBc proteins. By combining these data with primary sequence alignments, secondary structure prediction, and three-dimensional modeling, we propose a model for the fold of DHBc. Its major features are a HBc-like two-domain structure with an assembly domain comprising the first about 185 amino acids and a C-terminal nucleic acid binding domain (CTD), connected by a morphogenic linker region that is longer than in HBc and extends into the CTD. The assembly domain shares with HBc a framework of four major ␣-helices but is decorated at its tip with an extra element that contains at least one helix and that is made up only in part by the previously predicted insertion sequence. All subelements are interconnected, such that structural changes at one site are transmitted to others, resulting in an unexpected variability of particle morphologies. Key features of the model are independently supported by the accompanying epitope mapping study. These data should be valuable for functional studies on the impact of core protein structure on virus replication, and some of the mutant proteins may be particularly suitable for higher-resolution structural investigations.Hepatitis B viruses (HBVs), or hepadnaviruses, comprise a family of small enveloped DNA-containing viruses that replicate through reverse transcription (2). HBV, the causative agent of B-type hepatitis in humans, is the prototype of the orthohepadnaviruses which infect selected mammals, while duck HBV (DHBV) is the prototype of the avihepadnaviruses, which are endemic in some bird species (16). Overall, genome organization and replication mechanism of both genera are closely related; hence, DHBV serves as an important model hepadnavirus (43).However, although the DHBV genome is even smaller than that of HBV (3.0 kb versus 3.2 kb), its core protein (DHBc) is substantially larger (262 versus 183 or 185 amino acids) than that of HBV (HBc). Both core proteins are the sole building blocks for the viral capsid shell. The capsids are actively involved in reverse transcription (21, 33, 55) and genome trafficking (23); are the substrate for various phosphorylation and dephosphorylation events (1,17,25,32,37,57); and provide interaction sites, regulated by the maturation state of the packaged genome (47), for envelopment by the surface proteins (9). Evidently, the short HBc sequence fully supports these multiple functions; hence, the biological reasons behind the larger size of the avihepadnavirus core proteins are enigmatic. Knowledge of the DHBc structure would be crucial to understand this unresolved issue, and it might help to exploit the experimental advantages of DHBV (43) fo...