DSSR-PyMOL cartoon-block schematics: PDB entry 1l1w

PDB-id

1l1w; DSSR-derived features in text and JSON formats

Class

RNA

Method

NMR

Summary

NMR structure of a srp19 binding domain in human srp RNA

Reference

Sakamoto T, Morita S, Tabata K, Nakamura K, Kawai G (2002): "Solution structure of a SRP19 binding domain in human SRP RNA." J.Biochem.(Tokyo), 132, 177-182.

Abstract

Assembly of the human signal recognition particle (SRP) requires SRP19 protein to bind to helices 6 and 8 of SRP RNA. In the present study, structure of a 29-mer RNA composing the SRP19 binding site in helix 6 was determined by NMR spectroscopy. The two A:C mismatches were continuously stacked to each other and formed wobble type A:C base pairs. The GGAG tetraloop in helix 6 was found to adopt a similar conformation to that of GNRA tetraloop, suggesting that these tetraloops are included in an extensive new motif GNRR. Compared with the crystal structure of helix 6 in complex with SRP19 determined previously, the GGAG tetraloop in the complex was found to adopt a similar conformation to the free form, although the loop structure becomes more open upon SRP19 binding. Thus, SRP19 is thought to recognize the overall fold of the GGAG loop.