Fig. 5: Env cleavage frees the gp120 C-terminus to assume its position in the membrane-proximal base.

a The linear distances (LDs) between the last resolved gp120 C-terminal residue and the first resolved gp41 N-terminal residue in the protomers of the uncleaved HIV-1_JR-FL Env(-) trimer (PDB ID: 7N6U)²⁵, the cleaved AE2 Env timer (PDB ID: 8FAE)⁴¹, the cleaved Tri FPPR.1 Env trimer and the cleaved Tri FPPR.2 Env trimer are shown. LD was measured from C_α atom to C_α atom of the indicated gp120 and gp41 amino acid residues. N is the number of residues available to fill the gap and equals the number of unresolved residues + 1. The linear distance per residue (LD/N) represents the average span of an amino acid residue required to bridge the unresolved gap surrounding the Env cleavage site, in the absence of cleavage. b The relationships between the last resolved gp120 C-terminal residue and LD/N (left panel) and between the first resolved gp41 N-terminal residue and LD/N (right panel) are shown. The distance spanned by an amino acid residue in a fully extended peptide strand (3.4 Å) is marked by the red horizontal line. For LD/N values that exceed this physical limit, Env cleavage would be required to obtain the conformations of gp120 and gp41 observed in the structures. The degree of order in the gp120 C-terminus, reflected in the extent of the residues resolved in the structures, strongly correlates with the LD/N values. The Spearman rank order correlation coefficients (r_S) and two-tailed P values are shown. c Views of the membrane-proximal region from the Tri FPPR.1 and Tri FPPR.2 Env structures are shown, illustrating the relationship of the ordered gp120 C-termini to the MPER_N helices of the gp41 subunits from the same protomer. In the Tri FPPR.1 model on the left, gp120.C (light green) and gp41.D (dark green) chains are shown. In the Tri FPPR.2 model on the right, gp120.A (salmon) and gp41.B (red) chains are shown. In both cases, based on LD/N values greater than 3.4 Å, the observed conformations of the gp120 C-termini in the membrane-proximal base of the Tri FPPR Env trimers could only occur after Env cleavage. d Env sequences and structural relationships near the gp120-gp41 cleavage site (black triangle) are summarized. Env sequences that are disordered in the analyzed structures are indicated by wavy lines. Note that the degree of order in the gp120 C ­terminus (residues 506-511) is dependent both on Env cleavage and on the degree of order in the MPER of the same protomer.