Structural basis of diverse substrate recruitment by the HIV-1 Vpr-hijacked CRL4(VprBP) E3 ligase

HIV-1 hijacks the host CUL4-RING E3 ligase (CRL4) complex to trigger the degradation of various restriction factors. The viral accessory protein Vpr is the key protein that recruits diverse substrates to the receptor VprBP for proteasomal degradation. However, the underlying molecular mechanism remains poorly understood. Here, we characterize the molecular architecture of the DDB1-VprBP substrate recognition unit alone and in complex with different Vpr-substrates. Our results pinpoint that the LisH domain of VprBP mediates the DDB1-VprBP dimerization. Of note, the Armadillo-like (ARM-like) domains of VprBP adopt either an “up” or “down” conformation that may assist in accommodating Vpr-substrates of divergent stoichiometries and sizes. When bound to the small Vpr substrate UNG2, the two “up” ARM-like domains wrap around and directly interact with two symmetrical UNG2 molecules. Intriguingly, the ARM-like domains adopt a “down” conformation when bound to the larger TET2 fragment. Our structures highlight that the conformational dynamics of VprBP could enable the DDB1-VprBP complex to mediate the degradation of diverse Vpr-bound host factors. These findings could facilitate the structure-guided development of CRL4(VprBP)-based targeted protein degradation.