The identification of a novel interaction site for the human immunodeficiency virus capsid on nucleoporin 153

Human immunodeficiency virus type-1 (HIV-1) can infect non-dividing cells by passing through the selective permeability barrier of the nuclear pore complex. The viral capsid is essential for successfully delivering the HIV-1 genome into the nucleus. Nucleoporin 153 (NUP153) interacts with the HIV-1 capsid via a C-terminal capsid-binding motif (hereafter named CbM.1) to licence HIV-1 nuclear ingress. Deletion or mutation of CbM.1 in NUP153 causes a reduction in capsid interaction but does not prevent HIV-1 nuclear ingress or completely block capsid interaction. This paper combines molecular modelling with biochemical and HIV infection assays to identify capsid-binding motif 2 (CbM.2) in the C-terminus of NUP153 that is similar in sequence to CbM.1. CbM.2 has an FG dipeptide motif predicted to interact with a hydrophobic pocket in capsid protein (CA) hexamers similar to CbM.1. CA hexamers can interact with CbM.2, and the deletion of both CbM.1 and CbM.2 results in a lower capsid interaction than a single CbM.1 deletion. The loss of CbM.1 is complemented by CbM.2, an interaction dependent on the FG motif. In the context of the nuclear pore complex, a loss-of-function mutation in CbM.1 reduces HIV nuclear ingress as measured by transduction and 2-LTR circles, whereas the mutation of CbM.2 causes a large increase in 2-LTR circles. Our results highlighted a previously unidentified FG dipeptide-containing motif (CbM.2) in NUP153 that binds the HIV-1 capsid at the common hydrophobic pocket on CA hexamers.