# Structural understanding of the HIV-1 reverse transcription initiation process

> **NIH NIH R01** · HARVARD UNIVERSITY · 2022 · $604,947

## Abstract

Abstract
In retroviruses, reverse transcription is initiated from an intermolecular duplex primer formed
by nucleocapsid-driven annealing of the U5-primer binding site (U5-PBS) region of the genome
with a host tRNA. However, the structure of this critical complex, and how reverse transcriptase
(RT) interacts with it is largely unknown. The structure of the HIV-1 complex presented in this
proposal shows that four tandem GNRA modules in U5-PBS spatially organizes the complex by
making continuous tetraloop-receptor docking interactions: one engages a rearranged tRNA, one
sequesters the initiation site, and two sequester the 18-bp primer to inhibit RT binding. Thus, in
contrast to the widely accepted model that a single RT molecule recognizes this complex to
initiate transcription, our data show that, in fact, two molecules of RT are required to bind in a
step-wise manner to release the repressed state and ensure accurate initiation: the first extensively
interacts with the U5 stem and acts as a remodeler, allowing for the subsequent one to bind the
canonical 18-bp primer and perform the enzymatic activity. Manipulation of the architecture, the
remodeling process, or competition with nucleocapsid, leads to severe loss of initiation accuracy.
Thus, this study redefines our basic understanding of HIV reverse transcription initiation; assigns
RT a structural remodeler role, separate from its enzymatic function; and indicates that the unique
mechanism may contribute to the control of start of DNA synthesis in virions. The aims will be:
(#1) to further detail the mechanism by mutational analysis, (#2) to understand the structural role
of NC and (#3) to determine the structures of the remodeler RT and enzymatic RT bound to the
U5-PBS:tRNAlys complex.

## Key facts

- **NIH application ID:** 10547906
- **Project number:** 1R01AI167684-01A1
- **Recipient organization:** HARVARD UNIVERSITY
- **Principal Investigator:** Victoria Manuel D'Souza
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $604,947
- **Award type:** 1
- **Project period:** 2022-08-01 → 2026-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10547906

## Citation

> US National Institutes of Health, RePORTER application 10547906, Structural understanding of the HIV-1 reverse transcription initiation process (1R01AI167684-01A1). Retrieved via AI Analytics 2026-05-31 from https://api.ai-analytics.org/grant/nih/10547906. Licensed CC0.

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