Bacillus cereus is a Gram-positive, aerobic bacterium that forms highly resilient endospores encased in a multi-layered protective coat. Within the endospore, SpoIVA is localized to the basement layer of the spore coat via the direct interaction with the basement-localized protein SpoVM. In this study, we employed AlphaFold3, an AI-powered structural prediction program, to model the 3D structures of SpoIVA’s functional oligomers and to predict the complex structure of SpoIVA bound to SpoVM. Our findings identified a Y-shaped symmetric structure of the SpoIVA dimer, stabilized by interactions within its C-terminal domain, with SpoVM binding specifically on the C-terminal region of SpoIVA. AlphaFold3 further predicted an ATP-dependent oligomerization structure associated with the N-terminal domain of SpoIVA. The MD simulation suggested the dynamic structural nature of the SpoIVA oligomers. These results deepen our understanding of the structural and functional relationships among these spore-forming proteins, offering new insights into their roles in endospore architecture.