Sites of recurrent cell-culture mutations mapped on Env’s structure.

<p>The 25 sites from <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006114#ppat.1006114.g002" target="_blank">Fig 2B</a> where the mutation frequency increased >3-fold in at least two replicates after cell-culture passage. <b>(A)</b> Trimeric Env (PDB 5FYK [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006114#ppat.1006114.ref073" target="_blank">73</a>]) with one monomer in grey and the others in white, oriented so the membrane-proximal region is at the bottom. Sites of cell-culture mutations are shown as spheres, colored red-to-blue according to primary sequence. Most of these sites fall in one of three clusters. Mutations in the first cluster disrupt potential glycosylation sites at Env’s apex. The second cluster includes or is adjacent to sites where mutations are known to affect Env’s conformational dynamics [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006114#ppat.1006114.ref074" target="_blank">74</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006114#ppat.1006114.ref075" target="_blank">75</a>]. <b>(B)</b> The third cluster is near the co-receptor binding surface. This panel shows an apex-down view of monomeric gp120 (grey) in complex with CD4 (green) (PDB 3JWD [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006114#ppat.1006114.ref048" target="_blank">48</a>]). Sites of recurrent cell-culture mutations are shown as spheres colored according to primary sequence as in panel A. The black bar indicates cropping of CD4. <b>(C)</b> The same view as panel B, but the spheres now show sites known to affect binding to CXCR4 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006114#ppat.1006114.ref010" target="_blank">10</a>] or CCR5 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006114#ppat.1006114.ref076" target="_blank">76</a>]. Note the extensive overlap between the spheres in this panel and panel B.