3ID5

Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA

Summary for 3ID5

• Entry DOI: 10.2210/pdb3id5/pdb
• Related: 3ID6
• Descriptor: Pre mRNA splicing protein, Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase, 50S ribosomal protein L7Ae, ... (5 entities in total)
• Functional Keywords: c/d guide rna, 2'-o-methylation, coiled-coil, methyltransferase, rna-binding, rrna processing, transferase, trna processing, ribonucleoprotein, ribosomal protein, splicing-transferase-ribosomal protein-rna complex, transferase-ribosomal protein-rna complex, transferase/ribosomal protein/rna
• Biological source: Sulfolobus solfataricus; More
• Total number of polymer chains: 8
• Total formula weight: 192686.62

Authors

Ye, K. (deposition date: 2009-07-20, release date: 2009-08-25, Last modification date: 2024-05-29)

Primary citation

Ye, K.,Jia, R.,Lin, J.,Ju, M.,Peng, J.,Xu, A.,Zhang, L.
Structural organization of box C/D RNA-guided RNA methyltransferase.
Proc.Natl.Acad.Sci.USA, 106:13808-13813, 2009

PubMed Abstract: Box C/D guide RNAs are abundant noncoding RNAs that primarily function to direct the 2'-O-methylation of specific nucleotides by base-pairing with substrate RNAs. In archaea, a bipartite C/D RNA assembles with L7Ae, Nop5, and the methyltransferase fibrillarin into a modification enzyme with unique substrate specificity. Here, we determined the crystal structure of an archaeal C/D RNA-protein complex (RNP) composed of all 3 core proteins and an engineered half-guide RNA at 4 A resolution, as well as 2 protein substructures at higher resolution. The RNP structure reveals that the C-terminal domains of Nop5 in the dimeric complex provide symmetric anchoring sites for 2 L7Ae-associated kink-turn motifs of the C/D RNA. A prominent protrusion in Nop5 seems to be important for guide RNA organization and function and for discriminating the structurally related U4 snRNA. Multiple conformations of the N-terminal domain of Nop5 and its associated fibrillarin in different structures indicate the inherent flexibility of the catalytic module, suggesting that a swinging motion of the catalytic module is part of the enzyme mechanism. We also built a model of a native C/D RNP with substrate and fibrillarin in an active conformation. Our results provide insight into the overall organization and mechanism of action of C/D RNA-guided RNA methyltransferases.

PubMed: 19666563
DOI: 10.1073/pnas.0905128106

Experimental method

X-RAY DIFFRACTION (4.01 Å)