Central to our understanding of human immunodeficiency virus-induced fusion is the high resolution structure of fragments of the gp41 fusion protein folded in a low energy core conformation. However, regions fundamental to fusion, like the fusion peptide (FP), have yet to be characterized in the context of the cognate protein regardless of its conformation. Based on conformation-specific monoclonal antibody recognition, we identified the polar region consecutive to the N36 fragment as a stabilizer of trimeric coiled-coil assembly, thereby enhancing inhibitory potency. This tertiary organization is retained in the context of the hydrophobic FP (N70 fragment). Our data indicate that the N70 fragment recapitulates the expected organization of this region in the viral fusion intermediate (N-terminal half of the pre-hairpin intermediate (N-PHI)), which happens to be the prime target for fusion inhibitors. Regarding the low energy conformation, we show for the first time core formation in the context of the FP (N70 core). The ␣-helical and coiled-coil stabilizing polar region confers substantial thermal stability to the core, whereas the hydrophobic FP does not add further stability. For the two key fusion conformations, N-PHI and N70 core, we find that the FP adopts a nonhelical structure and directs higher order assembly (assembly of coiled coils in N-PHI and assembly of bundles in the N70 core). This supra-molecular organization of coiled coils or folded cores is seen only in the context of the FP. This study is the first to characterize the FP region in the context of the folded core and provides a basic understanding of the role of the elusive FP for key gp41 fusion conformations.The crystal structure of the HIV 2 gp41 core, presented nearly a decade ago (1-3), served as the basis for the following: (i) models describing gp41 conformational changes during its fusogenic activity (4, 5); (ii) the molecular mechanism describing the ability of exogenous gp41 N-and C-helix fragments to arrest fusion (6, 7); and (iii) design of next generation gp41-derived fusion inhibitors targeting both N-terminal heptad repeat (NHR) and C-terminal heptad repeat (CHR) viral targets (8 -10). Despite extensive efforts to characterize gp41, high resolution structures lack the N-terminal and membraneactive fusion peptide (FP) region, and our understanding of this fundamentally essential region is likewise limited.Prior to fusion, gp41 is held in a metastable state by the surface subunit gp120, and the complex is organized as a trimer visualized as spikes on the virion surface (11). Following receptors binding by gp120, gp41 is freed from metastable constraints (12) and adopts an extended conformation (pre-hairpin intermediate (PHI)) characterized by exposed NHR and CHR regions (8, 13). Collapse of the PHI into a thermostable six-helix bundle (SHB) or core conformation, formed by packing of CHR helices in an anti-parallel manner into hydrophobic grooves of the NHR trimeric parallel coiled coil (1), is believed to draw together viral and c...