HIV-1 Rev Response Element (RRE) Stem-Loop II (SLII)

Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

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

Tipo, J.Gottipati, K.Slaton, M.Gonzalez-Gutierrez, G.Choi, K.H.

(2024) Nat Commun 15: 4198-4198

  • DOI: https://doi.org/10.1038/s41467-024-48162-y
  • Primary Citation of Related Structures:  

  • PubMed 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.

  • Organizational Affiliation

    Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX, 77555, USA.

Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold
A, B
134HIV whole-genome vector AA1305#18
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.85 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.782α = 90
b = 81.314β = 99.14
c = 81.372γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
XDSdata scaling
PHENIXmodel building
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI187856

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release