page_title: HIV Rev response element
section_title: Stem IIB: a high-affinity binding site
hierarchical_section_title: HIV Rev response element / Secondary Structure and Rev Recognition / Stem IIB: a high-affinity binding site
caption_attribution_description: This is the structure of the Rev ARM in complex with IIB.
context_page_description: The HIV-1 Rev response element is a highly structured, ~350 nucleotide RNA segment present in the Env coding region of unspliced and partially spliced viral mRNAs. In the presence of the HIV-1 accessory protein Rev, HIV-1 mRNAs that contain the RRE can be exported from the nucleus to the cytoplasm for downstream events such as translation and virion packaging.
context_section_description: Stem IIB is a site on the RRE which Rev binds with high affinity and specificity.  The structure of an isolated stem IIB bound to a peptide corresponding to a Rev-ARM has been solved by NMR. This structure reveals an RNA A-form major groove widened by purine-purine base pairs at the purine-rich bulge to accommodate the a-helical Rev-ARM. Binding is achieved through a combination of base-specific contacts and electrostatic contacts with the phosphate backbone (see figure).  More recent studies have identified another region on the RRE, stem IA, that binds Rev in a specific manner, but with a 5-fold weaker affinity than stem IIB.
caption: Rev-ARM/IIB structure. (Left) Stem IIB RNA(red) A-‐form major groove cradling the Rev-‐ARM α-‐helix (blue). The Rev-ARM is a short peptide that represents the RNA binding domain of Rev. (Right) A rotated view showing the purine-‐purine base pairs (yellow) that widen the RNA major groove.
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