7XPL

Crystal structure of a C/D-free RNA-guided RNA 2'-O-methyltransferase

Summary for 7XPL

• Entry DOI: 10.2210/pdb7xpl/pdb
• Descriptor: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit, Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase, BMG3 RNA strand A, ... (7 entities in total)
• Functional Keywords: 2'-o-methylation, guide rna, rnp, rna binding protein, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Saccharolobus solfataricus; More
• Total number of polymer chains: 8
• Total formula weight: 167575.97

Authors

Wang, J.,Ye, K. (deposition date: 2022-05-04, release date: 2022-10-05, Last modification date: 2023-11-29)

Primary citation

Wang, J.,Yang, Z.,Ye, K.
Methylation guide RNAs without box C/D motifs.
Rna, 28:1597-1605, 2022

PubMed Abstract: Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The defining feature of methylation guide RNAs is two sets of box C and D motifs that form kink-turn structures specifically recognized by L7Ae family proteins. Here, we engineered a new type of methylation guide that lacks C/D motifs and requires no L7Ae for assembly and function. We determined a crystal structure of a bipartite C/D-free guide RNA in complex with Nop5, fibrillarin and substrate in the active form at 2.2 Å resolution. The stems of new guide RNAs functionally replace C/D motifs in Nop5 binding, precisely placing the substrate for site-specific modification. We also found that the bipartite architecture and association of L7Ae with C/D motifs enhance modification when association of guide RNAs or substrates is weak. Our study provides insights into the variations, robustness and possible evolutionary path of methylation guide RNAs.

PubMed: 36127125
DOI: 10.1261/rna.079379.122

Experimental method

X-RAY DIFFRACTION (2.213 Å)