Fig. 10

Structural modeling of the covariation network in the revertant Env. a Mapping amino acids 202, 305, and 328 on the structure of the crystallographic structure of HIV-1 Env, obtained on cleaved gp140 SOSIP trimers by Julien et al. [17]. gp120, blue; gp41, bronze with the transmembrane portion schematically drawn as a cylinder. Dotted black lines indicate the border between the structure determined in Ref. [17] and the parts drawn by us. Orange spheres indicate amino acids 305 and 328, purple spheres give the location of amino acid 202. b Mapping amino acids 202, 305, and 328 on the structure of the HIV-1 Env, obtained by Cryo-EM on cleaved gp140 SOSIP trimers by Bartesaghi et al. [19]. gp120 blue, bridging sheet red; gp41, bronze with the transmembrane portion schematically drawn as a cylinder. Dotted black lines indicate the border between the structure determined in Ref. [19] and the parts drawn by us. The putative folding of the V3 stem is drawn in blue for one monomer only, for sake of clarity (the positions of the two other V3 stems are indicated with blue arrows). Orange spheres indicate amino acids 305 (middle of the V3 stem) and 328 (base of the V3 stem), purple spheres give the location of amino acid 202. One molecule of CCR5 is schematically drawn in green (not in scale). Cell and viral membranes are schematically drawn as black lines. In the black box is depicted the docking of the sulfur-tyrosine of 412d antibody (mimicking CCR5) in the V3 loop as described by Huang et al. [23]. 412d is drawn in bronze with the sulfur in yellow and the oxygen atoms in red. The cage of lateral chains from the amino acids of V3 that surround and bind the sulfur-tyrosine is highlighted in deep blue. Amino acids 305 and 328 are highlighted in yellow