Architecture of an HIV-1 reverse transcriptase initiation complex

Reverse transcription of the HIV-1 RNA genome into double-stranded DNA is a central step in infection(1) and a common target of antiretrovirals(2). The reaction is catalyzed by viral reverse transcriptase (RT)(3,4) that is packaged in an infectious virion along with 2 copies of dimeric viral genomic RNA(5) and host tRNA(Lys)(3), which acts as a primer for initiation of reverse transcription(6,7). Upon viral entry, initiation is slow and non-processive compared to elongation(8,9). Despite extensive efforts, the structural basis for RT function during initiation has remained a mystery. Here we apply cryo-electron microscopy (cryo-EM) to determine a three-dimensional structure of the HIV-1 RT initiation complex. RT is in an inactive polymerase conformation with open fingers and thumb and with the nucleic acid primer-template complex shifted away from the active site. The primer binding site (PBS) helix formed between tRNA(Lys)(3) and HIV-1 RNA lies in the cleft of RT and is extended by additional pairing interactions. The 5′ end of the tRNA refolds and stacks on the PBS to create a long helical structure, while the remaining viral RNA forms two helical stems positioned above the RT active site, with a linker that connects these helices to the RNase H region of the PBS. Our results illustrate how RNA structure in the initiation complex alters RT conformation to decrease activity, highlighting a potential target for drug action.