9A9V | pdb_00009a9v

All-atom model of the Rev Response RNA Element of HIV-1 generated by mutagenesis- and FRET-guided FARFAR2 model selection.

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.

PDB DOI: https://doi.org/10.2210/pdb9A9V/pdb
NAKB: 9A9V

Mutation(s): Yes

Deposited: 2025-05-06 Released: 2025-11-05
Deposition Author(s): Szewczyk, M., Loharch, S., Lopez-Nunez, S., Gallego J.

Integrative Structure Snapshot

Multi-Scale: No
Multi-State: No
Ordered-State: No
Deposited Models: 1
Representative Model: 1

wwPDB ValidationFull ReportSummary Report

This is version 1.0 of the entry. See complete history.

Literature

Insights About the Structure and Recognition Mechanism of the Rev Response Element of HIV-1 Revealed by FRET-monitored Mutagenesis and Modeling

Szewczyk, M.P., Loharch, S., Lopez-Nunez, S., Gallego J.

(2025) J Mol Biol 437

PubMed: 40976347 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2025.169451
Primary Citation of Related Structures:
9A9V

PubMed Abstract:
The complex between several monomers of the HIV-1 Rev protein and the Rev Response Element (RRE) in the viral RNA allows nuclear export of unspliced or singly-spliced viral transcripts, an essential step in the virus cycle that is not targeted by any of the currently marketed antiretroviral treatments. The RRE adopts a multi-domain structure whose three-dimensional details are currently unknown at atomic resolution. In order to shed light on RRE structure and on the mechanism of RRE-Rev complex assembly, we set up a method based on fluorescence resonance energy transfer (FRET) that has allowed us to measure RRE interdomain distance as a function of solution conditions and changes in helix length and junction nucleotides. By combining this information with all-atom ensemble modeling, comparative sequence analyses and electrophoretic band-shift assays assessing Rev association, we clarify the roles of helices and junctions on the spatial organization of RRE domains and RRE-Rev complex formation and propose an all-atom model of RRE structure consistent with the available evidence.

Organizational Affiliation

Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia 46001 Valencia, Spain; Escuela de Doctorado, Universidad Católica de Valencia 46001 Valencia, Spain.