Coronaviruses (CoVs) such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), SARS-CoV-1 and Middle East Respiratory Syndrome (MERS) has had major impact on global health and economy, causing outbreaks, epidemics and the prominent COVID-19 pandemic. These three CoVs encode an integral membrane envelope (E) protein involved in several aspects of the virus’ life cycle with importance on pathogenesis. PALS1 is a highly conserved cell polarity regulator vital in stabilising cell junction formation and dysregulation of polarity is associated with poor prognosis during viral infections. Previous studies established that CoVs E interacts with PALS1 via its C-terminal PDZ binding motif (PBM), leading to aggregation of polarity regulators and subsequent perturbation of host cell adhesion, proliferation, and signalling. Using isothermal titration calorimetry (ITC) we now show SARS-CoV-2 and SARS-CoV-1 E PBM interacts with PALS1 PDZ1 domain. We then determined crystal structures of SARS-CoV-2 and SARS-CoV-1 E PBM to PALS1 PDZ1, which establish a structural basis for E protein subversion of PALS1 mediated cell polarity signalling and provide the platform for mechanistic studies to examine E induced mislocalisation of PALS1 and the associated changes in cellular architecture.