Summary information and primary citation

PDB-id
1f5u; DSSR-derived features in text and JSON formats
Class
RNA
Method
NMR
Summary
Solution structure of the kissing dimer of h3 gacg stem-loop in the 5'-end dimerization signal of moloney murine leukemia virus genomic RNA
Reference
Kim CH, Tinoco Jr I (2000): "A retroviral RNA kissing complex containing only two G.C base pairs." Proc.Natl.Acad.Sci.USA, 97, 9396-9401. doi: 10.1073/pnas.170283697.
Abstract
The dimerization of viral RNA through noncovalent interactions at their 5' ends is a key step in the life cycle of retroviruses. In Moloney murine leukemia virus, three stem-loops are important in this process. One is a self-complementary tetraloop (H1), but the other two stem-loops (H2, H3) contain highly conserved GACG tetraloops that are not self-complementary sequences. Using two-dimensional NMR, we determined the structure of the H3 stem-loop. Surprisingly, it forms a stable, homodimeric kissing complex through only two intermolecular G small middle dotC base pairs. Cross-strand interactions of the adenines adjacent to the intermolecular G small middle dotC base pairs, plus unusual strong electrostatic interactions around the base pairs, contribute to the unexpected stability. This structure shows how even stem-loops without self-complementary sequences can facilitate the intermolecular recognition between two identical RNAs, and thus initiate dimerization and encapsidation of retroviral RNAs.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js