Structural characterization of human endogenous retrovirus integration and strand transfer inhibition

Human endogenous retroviruses (hERVs) are remnants of ancestral retroviral infections that have shaped the human genome through their capacity to mobilize and retrotranspose. Among these, hERV-K (HML-2) remains the most recently active family and its dysregulation is strongly associated with diverse cancers and neurodegenerative pathologies, yet the structural basis of its integration remains poorly understood. Here, we combine activity assays with high-resolution cryo-electron microscopy to resolve the hERV-K integration machinery in three distinct states: asymmetric target-DNA engagement, strand transfer, and pharmacological inhibition. Our structures reveal a compact architecture defined by a unique organization of the outer integrase domains, which distinguishes hERV-K from other known retroviral intasomes. Biochemical validation confirms the catalytic competence of this compact tetrameric assembly, which relies on specialized polar motifs to optimize synaptic stability while retaining sensitivity to competitive antagonism by strand transfer inhibitors. Notably, beyond canonical restriction by Raltegravir, we discovered that the drug binding stabilizes an unanticipated, “closed” conformation not observed in previously characterized intasomes. Together, these findings elucidate the molecular mechanism of endogenous retroviral integration and provide a structural framework for rational therapeutic targeting of hERV-K-driven diseases.