Long range pseudoknots

A long range pseudoknot is a pseudoknot containing a long loop region, and may be a mechanism of translational control.

Long range pseudoknot
Secondary structure of the long range pseudoknot
Identifiers
Rfam	RF01086
Other data
RNA type	Cis-reg
Domain(s)	Eukaryote Prokaryote
PDB structures	PDBe

A long range pseudoknot is thought to negatively regulate the translation of the IF3-L35-L20 operon in E. coli. This operon encodes the translation initiation factor IF-3 and ribosomal proteins L35 and L20. In this example, the RNA-RNA interaction occurs between nucleotides separated by a 300 nucleotide loop region.^[1]

A long range pseudoknot is also believed to be required for the activity of the Neurospora VS ribozyme.^[2]