SNAP output for PDB entry 4n2s [SNAP web server]

PDB-id

4n2s; SNAP-derived features in text and JSON formats; DNAproDB

Class

splicing-RNA

Method

X-ray (3.0 Å)

Summary

Crystal structure of tha8 in complex with zm1a-6 RNA

Reference

Ke J, Chen RZ, Ban T, Zhou XE, Gu X, Tan MH, Chen C, Kang Y, Brunzelle JS, Zhu JK, Melcher K, Xu HE (2013): "Structural basis for RNA recognition by a dimeric PPR-protein complex." Nat.Struct.Mol.Biol., 20, 1377-1382. doi: 10.1038/nsmb.2710.

Abstract

Thylakoid assembly 8 (THA8) is a pentatricopeptide repeat (PPR) RNA-binding protein required for the splicing of the transcript of ycf3, a gene involved in chloroplast thylakoid-membrane biogenesis. Here we report the identification of multiple THA8-binding sites in the ycf3 intron and present crystal structures of Brachypodium distachyon THA8 either free of RNA or bound to two of the identified RNA sites. The apostructure reveals a THA8 monomer with five tandem PPR repeats arranged in a planar fold. The complexes of THA8 bound to the two short RNA fragments surprisingly reveal asymmetric THA8 dimers with the bound RNAs at the dimeric interface. RNA binding induces THA8 dimerization, with a conserved G nucleotide of the bound RNAs making extensive contacts with both monomers. Together, these results establish a new model of RNA recognition by RNA-induced formation of an asymmetric dimer of a PPR protein.