Structural Basis of CD4 Downregulation by HIV-1 Nef

Kwon, Y.; Kaake, R.; Echeverria, I.; Suarez, M.; Stoneham, C.; Ramirez, P. W.; Kress, J.; Singh, R.; Sali, A.; Krogan, N. J.; Guatelli, J.; Jia, X.

doi:10.1101/2020.04.21.054007

bioRxiv · 10.1101/2020.04.21.054007

Structural Basis of CD4 Downregulation by HIV-1 Nef

Kwon, Y.·Kaake, R.·Echeverria, I.·Suarez, M.·Stoneham, C.·Ramirez, P. W.·Kress, J.·Singh, R.·Sali, A.·Krogan, N. J.·Guatelli, J.·Jia, X.

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Abstract

The HIV-1 protein Nef suppresses multiple immune surveillance mechanisms to promote viral pathogenesis1. Individuals infected with HIV-1 encoding defective nef genes do not develop AIDS for decades2,3. 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 infectivity4; it interferes with the release of new virions5,6; and it causes vulnerability to superinfection, causing premature cell death and limiting viral productivity7. 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 antibodies8-10. 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 degradation11. Surface-expressed CD4, in contrast, is targeted by Nef for endocytosis and lysosomal degradation12-15. Nefs effect on CD4 involves hijacking of clathrin adaptor complex 2 (AP2)-dependent endocytosis16,17. Although how Nef associates with a part of the tetrameric AP2 is understood18, 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 Nefs activities and sensitize the virus to immune clearance

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Kwon, Y., Kaake, R., Echeverria, I., Suarez, M., Stoneham, C., Ramirez, P. W., Kress, J., Singh, R., Sali, A., Krogan, N. J., Guatelli, J., Jia, X.. 2020-04-23. Structural Basis of CD4 Downregulation by HIV-1 Nef. https://doi.org/10.1101/2020.04.21.054007

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