Summary information and primary citation

PDB-id
1jbr; SNAP-derived features in text and JSON formats; DNAproDB
Class
hydrolase-RNA
Method
X-ray (2.15 Å)
Summary
Crystal structure of the ribotoxin restrictocin and a 31-mer srd RNA inhibitor
Reference
Yang X, Gerczei T, Glover LT, Correll CC (2001): "Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping." Nat.Struct.Biol., 8, 968-973. doi: 10.1038/nsb1101-968.
Abstract
The cytotoxin sarcin disrupts elongation factor binding and protein synthesis by specifically cleaving one phosphodiester bond in ribosomes. To elucidate the molecular basis of toxin action, we determined three cocrystal structures of the sarcin homolog restrictocin bound to different analogs that mimic the target sarcin/ricin loop (SRL) structure of the rat 28S rRNA. In these structures, restrictocin contacts the bulged-G motif and an unfolded form of the tetraloop of the SRL RNA. In one structure, toxin loops guide selection of the target site by contacting the base critical for recognition (G4319) and the surrounding S-shaped backbone. In another structure, base flipping of the tetraloop enables cleavage by placing the target nucleotide in the active site with the nucleophile nearly inline for attack on the scissile bond. These structures provide the first views of how a site-specific protein endonuclease recognizes and cleaves a folded RNA substrate.

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

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