The initial atomic model templates of all three particles and immune complexes were generated from homology modeling upon CVA6 [Protein Data Bank (PDB) code: 5XS4 (17)] and its immune complex [PDB code: 5XS7 (17)] by Accelrys Discovery Studio software (51). Then, the template was docked into a segmented volume (enclosing a promoter) of final cryo-EM maps (viral particles or immune complexes) using Chimera (52). The sequence assignment was guided by the clearly recognizable features for bulky side chains, such as Phe, Tyr, Arg, and Trp. The manual model building and automatic refinement were alternately and iteratively performed in Coot (53) and the module phenix.real_space_refine in PHENIX (53, 54). The refined protomer was docked into the density of six neighboring protomers, which were then treated as a whole model for further optimization to avoid clashes between protomers. Model statistics including bond lengths, bond angles, all atom clashes, rotamer statistics, Ramachandran plot statistics, etc., were closely inspected with Coot during the whole process. The final models were validated using Molprobity (55) and EMRinger (56). Multiple sequence alignments were performed using ClustalW and ClustalX (version 2) on the EBI server, and the results were generated using ESPript (57). Figures were prepared with Chimera (52) and PyMOL (58). The roadmap of Fabs footprint was displayed with the program Radial Interpretation of Viral Electron density Maps (RIVEM) (59). The interactions between virus capsid and Fab were inspected with the software CCP4 (60) and the PISA sever (www.ebi.ac.uk/pdbe/pisa). The intermolecular interactions were analyzed on the basis of the assumption that cutoff distances are 4 Å for a hydrogen bond and 3.5 Å for a salt bridge.

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