9DID

Rous sarcoma virus frameshifting pseudoknot RNA

Summary for 9DID

• Entry DOI: 10.2210/pdb9did/pdb
• Related: 9DIB
• Descriptor: frameshifting pseudoknot RNA, IRIDIUM HEXAMMINE ION, POTASSIUM ION, ... (5 entities in total)
• Functional Keywords: pseudoknot, retroviral rna, frameshifting, translation regulation, rna
• Biological source: Rous sarcoma virus - Prague C
• Total number of polymer chains: 2
• Total formula weight: 75840.63

Authors

Jones, C.P.,Ferre-D'Amare, A.R. (deposition date: 2024-09-05, release date: 2025-04-09, Last modification date: 2025-04-16)

Primary citation

Jones, C.P.,Ferre-D'Amare, A.R.
Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus-programmed ribosomal frameshifting element.
Proc.Natl.Acad.Sci.USA, 122:e2418418122-e2418418122, 2025

PubMed Abstract: A hallmark of retrovirus replication is the translation of two different polyproteins from one RNA through programmed -1 frameshifting. This is a mechanism in which the actively translating ribosome is induced to slip in the 5' direction at a defined codon and then continues translating in the new reading frame. Programmed frameshifting controls the stoichiometry of viral proteins and is therefore under stringent evolutionary selection. Forty years ago, the first frameshifting stimulatory element was discovered in the Rous sarcoma virus. The ~120 nt RNA segment was predicted to contain a pseudoknot, but its 3D structure has remained elusive. Now, we have determined cryoEM and X-ray crystallographic structures of this classic retroviral element, finding that it adopts a butterfly-like double-pseudoknot fold. One "wing" contains a dynamic pyrimidine-rich helix, observed crystallographically in two conformations and in a third conformation via cryoEM. The other wing encompasses the predicted pseudoknot, which interacts with a second unexpected pseudoknot through a toggle residue, A2546. This key purine switches conformations between structural states and tunes the stability of interacting residues in the two wings. We find that its mutation can modulate frameshifting by as much as 50-fold, likely by altering the relative abundance of different structural states in the conformational ensemble of the RNA. Taken together, our structure-function analyses reveal how a dynamic double pseudoknot junction stimulates frameshifting by taking advantage of conformational heterogeneity, supporting a multistate model in which high Shannon entropy enhances frameshifting efficiency.

PubMed: 40172966
DOI: 10.1073/pnas.2418418122

Experimental method

X-RAY DIFFRACTION (2.8 Å)