3P22: Crystal Structure Of The Ene, A Viral Rna Stability Element, In Complex With A9 Rna

Kaposi's sarcoma-associated herpesvirus produces a highly abundant, nuclear noncoding RNA, polyadenylated nuclear (PAN) RNA, which contains an element that prevents its decay. The 79-nucleotide expression and nuclear retention element (ENE) was proposed to adopt a secondary structure like that of a box H/ACA small nucleolar RNA (snoRNA), with a U-rich internal loop that hybridizes to and protects the PAN RNA poly(A) tail. The crystal structure of a complex between the 40-nucleotide ENE core and oligo(A)(9) RNA at 2.5 angstrom resolution reveals that unlike snoRNAs, the U-rich loop of the ENE engages its target through formation of a major-groove triple helix. A-minor interactions extend the binding interface. Deadenylation assays confirm the functional importance of the triple helix. Thus, the ENE acts as an intramolecular RNA clamp, sequestering the PAN poly(A) tail and preventing the initiation of RNA decay.
PDB ID: 3P22Download
MMDB ID: 87209
PDB Deposition Date: 2010/10/1
Updated in MMDB: 2010/12
Experimental Method:
x-ray diffraction
Resolution: 2.5  Å
Source Organism:
synthetic construct
Biological Unit for 3P22: dimeric; determined by author and by software (PISA)
Molecular Components in 3P22
Label Count Molecule
Nucleotides(2 molecules)
Core ENE Hairpin From Kshv PAN RNA
Molecule annotation
Oligo(a)9 RNA
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB