Structural Basis of CD4 Downregulation by HIV-1 Nef

The HIV-1 protein Nef suppresses multiple immune surveillance mechanisms to promote viral pathogenesis 1 . Individuals infected with HIV-1 encoding defective nef genes do not develop AIDS for decades 2,3 . A key target of Nef is the cellular receptor CD4. Although essential for viral entry into host cells, CD4 is problematic for the virus later in its replication cycle: CD4 disrupts processing of the viral glycoprotein, Env, inhibiting infectivity 4 ; it interferes with the release of new virions 5,6 ; and it causes vulnerability to superinfection, causing premature cell death and limiting viral productivity 7 . Furthermore, binding of CD4 to Env exposes otherwise-concealed Env epitopes, rendering infected cells more susceptible to antibody-dependent cellular cytotoxicity and virus particles more susceptible to neutralizing antibodies 8-10 . HIV-1 has evolved strategies to mitigate these problems. Newly synthesized CD4 is targeted in the endoplasmic reticulum by the viral Vpu protein for proteasomal degradation 11 . Surface-expressed CD4, in contrast, is targeted by Nef for endocytosis and lysosomal degradation 12-15 . Nef’s effect on CD4 involves hijacking of clathrin adaptor complex 2 (AP2)-dependent endocytosis 16,17 . Although how Nef associates with a part of the tetrameric AP2 is understood 18 , a complete understanding of the interaction, especially how CD4 is sequestered by Nef into a complex with AP2, has remained elusive. Here, we present a high-resolution crystal structure that describes the underlying mechanism. An intricate combination of conformational changes occurs in both Nef and AP2 to enable CD4 binding and downregulation. Strikingly, a pocket on Nef previously identified as crucial for recruiting class I MHC is also responsible for recruiting CD4, revealing a potential approach to inhibit two of Nef’s activities and sensitize the virus to immune clearance