Extended Data Figure 3 : A model of eCD4-Ig bound to the HIV-1 Env trimer.

From: AAV-expressed eCD4-Ig provides durable protection from multiple SHIV challenges

Extended Data Figure 3

a, The structure (2QAD) of gp120 (YU2 isolate) bound to the tyrosine-sulfated CD4i antibody 412d and CD4 domains 1 and 2 (ref. 10), was fitted into a cryoelectron micrograph of the HIV-1 envelope glycoprotein trimer (Env; Bal isolate) bound to CD4 (ref. 48). gp120 and CD4 domains 1 and 2 are shown in blue and red, respectively. 412d sulfotyrosines are represented as green (carbon), red (oxygen) and yellow (sulphur) spheres. The remainder of 412d was excluded for clarity. b, The same structure shown in a rotated 90° about the horizontal axis. Note that the sulfotyrosine-binding pockets are proximal to the trimer axis, whereas the C terminus of CD4 domain 2 is distal from the trimer axis, preventing both CD4 domains of CD4-Ig from simultaneously binding the same Env trimer. c, A model of how eCD4-Ig may associate with Env is presented. The Fc domain of human IgG1 (1FCC, cyan)49 was positioned to be proximal to the gp120 sulfopeptide-binding pocket occupied by sulfotyrosine 100 (Tys 100) of the 412d heavy chain while avoiding steric interaction with Env. Tys 100 occupies a pocket in gp120 thought to bind CCR5 sulfotyrosine 10 (ref. 50). This pocket is also critical for binding of CCR5mim1 and CCR5mim 2 (refs 20, 22). In this model, the Fc domain is oriented to allow each eCD4-Ig sulfopeptide to engage a different gp120 protomer24. A single CD4 domain also binds one of the sulfopeptide-bound protomers. Distances between the C terminus of CD4 and the N terminus of one Fc domain monomer (38.1 Å), between the C terminus of the Fc domain and Tys 100 pocket of the CD4-bound gp120 protomer (30.6 Å), and between the C terminus of the Fc domain and Tys 100 pocket of an adjacent gp120 protomer (33.3 Å), are indicated. d, Residues not visible in the crystal structures used to construct this model are shown between brackets. In the model shown in c, these residues span the distances indicated. Note that these distances are well under the extension of a typical beta strand. CD4-, IgG1- and CCR5mim1-derived residues are shown in red, cyan, and green, respectively, with linker regions shown in black. Residues visible in the crystal structures, including the CCR5mim1 sulfotyrosine presumed to fill the Tys 100 pocket, are highlighted in grey. Modelling was performed using UCSF Chimera version 1.8.