High-resolution asymmetric structure of a Fab–virus complex reveals overlap with the receptor binding site

Abstract

Canine parvovirus is an important pathogen causing severe diseases in dogs, including acute hemorrhagic enteritis, myocarditis, and cerebellar disease. Overlap on the surface of parvovirus capsids between the antigenic epitope and the receptor binding site has contributed to cross-species transmission, giving rise to closely related variants. It has been shown that Mab 14 strongly binds and neutralizes canine but not feline parvovirus, suggesting this antigenic site also controls species-specific receptor binding. To visualize the conformational epitope at high resolution, we solved the cryogenic electron microscopy (cryo-EM) structure of the Fab–virus complex. We also created custom software, Icosahedral Subparticle Extraction and Correlated Classification, to solve a Fab–virus complex with only a few Fab bound per capsid and visualize local structures of the Fab-bound and -unbound antigenic sites extracted from the same complex map. Our results identified the antigenic epitope that had significant overlap with the receptor binding site, and the structures revealed that binding of Fab induced conformational changes to the virus. We were also able to assign the order and position of attached Fabs to allow assessment of complementarity between the Fabs bound to different positions. This approach therefore provides a method for using cryo-EM to investigate complementarity of antibody binding.

A cryo-ET survey of microtubules and intracellular compartments in mammalian axons

“…These structures were roughly spherical with angular edges. They appeared similar to virus capsids ( Goetschius et al, 2021 ; Vijayakrishnan et al, 2020 ), and so we call them virus-like capsids. Many contained discrete, globular densities in the lumen ( Fig.…”

Viral capsid, antibody, and receptor interactions: experimental analysis of the antibody escape evolution of canine parvovirus

“…Previous work revealed the interactions between mAb Fab14 and FabE and CPV-2 capsids at high resolution (Fig. 1A and B) (33,34). Here, we determined the selective pressure impose by those antibodies and defined the subsequent emergence of escape mutations in antibody and receptor binding sites (Fig.…”

“…Mouse or rat monoclonal antibodies (mAb) prepared against FPV, CPV-2, or CPV-2a capsids recognize many positions on the capsid surface, and cryoEM analysis of the binding sites of eight different rodent IgGs showed that their footprints covered about 65% of the capsid surface (1,17). Near-atomic resolution structures of some of these antibodies bound to CPV capsids have been obtained and confirm that both the antibody heavy and light chain complementarity determining regions (CDRs) contact multiple surface loops from different VP2 (or VP1) subunits (33,34). Antigenic variation in CPV-and FPV-related viruses have frequently been observed during their natural evolution (35)(36)(37), and escape mutations are readily selected by the growth of viruses in the presence of the mAbs (38,39).…”

“…Engineering the antigen-binding site of CPV-2-specific scFv-Fcs. Predicted antibody: capsid interactions were modeled on the cryoEM structures (33,34), and mutations selected using the swappa interactive tool available in UCSF Chimera X (45) following the Dunbrack model (46). New charged amino acid residues introduced into the antigen-binding sites were predicted to form distinct interactions with residues expressed on the CPV-2 capsid loops (Figs.…”

Cryo EM Analysis Reveals Inherent Flexibility of Authentic Murine Papillomavirus Capsids

“…A metadata file containing icosahedrally refined particle origins and orientations is required as input. The beta version of ISECC was used with cryoSPARC metadata files [ 17 , 26 ]. ISECC_subparticle_extract was used after icosahedral refinement to divide each particle image into subparticles [ 17 ].…”