Cryo-EM visualization of an exposed RGD epitope on adenovirus that escapes antibody neutralization

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Abstract
Interaction of the adenovirus penton base protein with αV integrins promotes virus entry into host cells. The location of the integrin binding sequence Arg‐Gly‐Asp (RGD) on human type 2 adenovirus (Ad2) was visualized by cryo‐electron microscopy (cryo‐EM) and image reconstruction using a mAb (DAV‐1) which recognizes a linear epitope, IRGDTFATR. The sites for DAV‐1 binding corresponded to the weak density above each of the five 22 Å protrusions on the adenovirus penton base protein. Modeling of a Fab fragment crystal structure into the adenovirus‐Fab cryo‐EM density indicated a large amplitude of motion for the Fab and the RGD epitope. An unexpected finding was that Fab fragments, but not IgG antibody molecules, inhibited adenovirus infection. Steric hindrance from the adenovirus fiber and a few bound IgG molecules, as well as epitope mobility, most likely prevent binding of IgG antibodies to all five RGD sites on the penton base protein within the intact virus. These studies indicate that the structure of the adenovirus particle facilitates interaction with cell integrins, whilst restricting binding of potentially neutralizing antibodies.