9C75 | pdb_00009c75

The crystal structure of HIV-1 Rev Response Element Stem-Loop II G34U mutant in complex with a Fab

PDB DOI: https://doi.org/10.2210/pdb9C75/pdb
NAKB: 9C75

Classification: RNA/IMMUNE SYSTEM
Organism(s): Homo sapiens, Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-06-10 Released: 2025-05-28
Deposition Author(s): Ojha, M., Koirala, D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free:
0.252 (Depositor), 0.251 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Mutation-driven RRE stem-loop II conformational change induces HIV-1 nuclear export dysfunction.

Ojha, M., Hudson, L., Photenhauer, A., Zang, T., Lerew, L., Ekesan, S., Daniels, J., Nguyen, M., Paudyal, H., York, D.M., Ohi, M.D., Marchant, J., Bieniasz, P.D., Koirala, D.

(2025) Nucleic Acids Res 53

PubMed: 40613716 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gkaf583
Primary Citation Related Structures:
9C2K, 9C75, 9E7D, 9E7E, 9E7G

PubMed Abstract:
The Rev response element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 (human immunodeficiency virus type 1) infection. However, the structures and mechanisms underlying this process remain largely unknown. Here, we determined the crystal structure of the HIV-1 RRE stem-loop II (SLII), revealing a unique three-way junction architecture in which the base stem (IIa) bifurcates into the stem-loops (IIb and IIc) to compose Rev binding sites. The crystal structures of various SLII mutants demonstrated that while some mutants retain the same "compact" fold as the wild type, other single-nucleotide mutants induce drastic conformational changes, forming an "extended" SLII structure. Through in vitro Rev binding assays and Rev activity measurements in HIV-1-infected cells using structure-guided SLII mutants designed to favor specific conformers, we showed that while the compact fold represents a functional SLII, the alternative extended conformation inhibits Rev binding and oligomerization and consequently stimulates HIV-1 RNA nuclear export dysfunction. The propensity of SLII to adopt multiple conformations as captured in crystal structures and their influence on Rev oligomerization illuminate emerging perspectives on RRE structural plasticity-based regulation of HIV-1 nuclear export and provide opportunities for developing anti-HIV drugs targeting specific RRE conformations.