The complement regulation protein CD46 is the primary attachment receptor for most species B adenoviruses (Ads). However, significant variability exists in sequence and structure among species B Ads in the CD46-binding regions, correlating with differences in affinity. Here, we report a structure-function analysis of the interaction of the species B Ad21 knob with the two N-terminal repeats SCR1 and SCR2 of CD46, CD46-D2. We have determined the structures of the Ad21 knob in its unliganded form as well as in complex with CD46-D2, and we compare the interactions with those observed for the Ad11 knob-CD46-D2 complex. Surface plasmon resonance measurements demonstrate that the affinity of Ad21 knobs for CD46-D2 is 22-fold lower than that of the Ad11 knob. The superposition of the Ad21 and Ad11 knob structures in complex with CD46-D2 reveals a substantially different binding mode, providing an explanation for the weaker binding affinity of the Ad21 knob for its receptor. A critical difference in both complex structures is that a key interaction point, the DG loop, protrudes more in the Ad21 knob than in the Ad11 knob. Therefore, the protruding DG loop does not allow CD46-D2 to approach the core of the Ad21 knob as closely as in the Ad11 knob-CD46-D2 complex. In addition, the engagement of CD46-D2 induces a conformational change in the DG loop in the Ad21 knob but not in the Ad11 knob. Our results contribute to a more profound understanding of the CD46-binding mechanism of species B Ads and have relevance for the design of more efficient gene delivery vectors.The 52 human adenovirus (Ad) serotypes are divided into seven species (species A to G) (20). Species B Ads are of interest, as they cause severe infections of the respiratory tract, urinary tract, and kidney as well as multiorgan system failure and death in immunocompromised patients (2,23,24). Species B Ads can be further grouped into subspecies B1 (Ad3, Ad7, Ad16, Ad21, and Ad50) and subspecies B2 (Ad11, Ad14, Ad34, and Ad35). Viruses in the two subspecies differ in their tropisms: while most B1 viruses cause ocular and/or acute respiratory tract infections, the B2 viruses primarily cause persistent infections of the urinary tract as well as eye infections, meningitis, and infections of the gastrointestinal tract (10,11,43). The subspecies B1 Ad21, which is the subject of this study, recently caused outbreaks of acute respiratory disease (28).Adenoviruses have a nonenveloped icosahedral capsid with a linear double-stranded DNA (46). The major capsid proteins are the hexon, the penton base, and the fiber. The trimeric fiber protein, which protrudes from each of the 12 capsid vertices, consists of three distinct domains: an N-terminal tail, an elongated shaft, and a globular knob. The knob mediates cellular attachment to the primary receptors CD46 (16,26,38), coxsackievirus and adenovirus receptor (CAR) (36), and sialic acid (3). Virus attachment is followed by internalization into the host cell via clathrin-coated endocytosis and macropinocytosis, triggered by ...