Factors controlling the dominance of antibody responses to specific sites in viruses and/or protein antigens are ill defined but can be of great importance for the induction of potent immune responses to vaccines. West Nile virus and other related important human-pathogenic flaviviruses display the major target of neutralizing antibodies, the E protein, in an icosahedral shell at the virion surface. Potent neutralizing antibodies were shown to react with the upper surface of domain III (DIII) of this protein. Using the West Nile virus system, we conducted a study on the immunodominance and functional quality of E-specific antibody responses after immunization of mice with soluble protein E (sE) and isolated DIII in comparison to those after immunization with inactivated whole virions. With both virion and sE, the neutralizing response was dominated by DIIIspecific antibodies, but the functionality of these antibodies was almost four times higher after virion immunization. Antibodies induced by the isolated DIII had an at least 15-fold lower specific neutralizing activity than those induced by the virion, and only 50% of these antibodies were able to bind to virus particles. Our results suggest that immunization with the tightly packed E in virions focuses the DIII antibody response to the externally exposed sites of this domain which are the primary targets for virus neutralization, different from sE and isolated DIII, which also display protein surfaces that are cryptic in the virion. Despite its low potency for priming, DIII was an excellent boosting antigen, suggesting novel vaccination strategies that strengthen and focus the antibody response to critical neutralizing sites in DIII.The availability of high-resolution structures is a prerequisite for understanding structural determinants of immunogenicity and immunodominance. Knowledge of factors that control and/or influence these properties of antigens can lead to an improvement of existing vaccines and the rational design of new vaccine antigens and regimens (13). Flaviviruses are among those human-pathogenic viruses for which detailed structural information is available through the combined use of X-ray crystallography and cryo-electron microscopy (cryo-EM) (25, 30, 36-38, 40, 49, 65). The most important representatives are the mosquito-borne yellow fever (YF), dengue (DEN), Japanese encephalitis (JE), and West Nile (WN) viruses, as well as tick-borne encephalitis (TBE) virus (14). These viruses have a significant impact on public health and the potential for emergence in new geographic regions, as exemplified by the expansion of WN virus in the Americas since its first introduction into the United States in 1999 (17). Human vaccines are in general use against YF virus (live attenuated), JE virus (live attenuated and inactivated whole virus), and TBE virus (inactivated whole virus) but not yet against DEN and WN viruses (48).Mature flavivirions are composed of an isometric capsid containing the positive-stranded RNA genome and a lipid envelope with two me...