Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site

Jerricho Tipo, Keerthi Gottipati, Michael Slaton, Giovanni Gonzalez-Gutierrez and Kyung H. Choi ()
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Jerricho Tipo: The University of Texas Medical Branch
Keerthi Gottipati: Indiana University
Michael Slaton: Indiana University
Giovanni Gonzalez-Gutierrez: Indiana University
Kyung H. Choi: The University of Texas Medical Branch

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract During HIV infection, specific RNA-protein interaction between the Rev response element (RRE) and viral Rev protein is required for nuclear export of intron-containing viral mRNA transcripts. Rev initially binds the high-affinity site in stem-loop II, which promotes oligomerization of additional Rev proteins on RRE. Here, we present the crystal structure of RRE stem-loop II in distinct closed and open conformations. The high-affinity Rev-binding site is located within the three-way junction rather than the predicted stem IIB. The closed and open conformers differ in their non-canonical interactions within the three-way junction, and only the open conformation has the widened major groove conducive to initial Rev interaction. Rev binding assays show that RRE stem-loop II has high- and low-affinity binding sites, each of which binds a Rev dimer. We propose a binding model, wherein Rev-binding sites on RRE are sequentially created through structural rearrangements induced by Rev-RRE interactions.

Date: 2024
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DOI: 10.1038/s41467-024-48162-y

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