Receptors are gatekeepers of information that transfer signals across membranes. Different steps of activation through conformational and compositional changes are necessary to fine-tune the downstream signalling, which are highly dynamic processes. G protein-coupled receptors (GPCRs) are ubiquitously expressed membrane proteins that are activated by endogenous ligands and involved in a variety of biological functions. Class B1 peptide hormone GPCRs have a broad range of regulatory metabolic effects and are therefore important drug targets. Recent advances in cryo-electron microscopy (cryo-EM) have enabled structure determination of the VPAC receptor family, which enhances our understanding of the molecular mechanisms of ligand binding and specificity. We solved high-resolution structures of active VPAC1R and PAC1R complexes to sub-3 Å average resolution, revealing atomic details of receptor interactions with different endogenous ligands. Using 3D variability analysis in CryoSPARC, we identified modes of conformational flexibility that differ between receptor-peptide pairs; these modes were further supported by molecular dynamics simulations (MD). This dynamic analysis allowed determination of key features for receptor activation and peptide selectivity. Moreover, the collective temporal structural information provides a platform for development of realistic and biologically relevant 3D animations, illustrating important steps involved in selective peptide binding and receptor signalling. To capture the conformational variability, we extrapolate trajectories of atomic coordinates that occur in cryo-EM 3D variability and MD and load these into Blender3D, an open-source 3D computer graphics software package. We can then combine these trajectory frames to create realistic and engaging movies of receptor activation in lipid membranes. The illustrative graphics and movies based on our experimental data can both inform drug development and provide templates for communication of complex concepts to a broader, non-expert audience.