3ICX
Crystal structure of Sulfolobus solfataricus Nop5 (135-380)
Summary for 3ICX
| Entry DOI | 10.2210/pdb3icx/pdb |
| Descriptor | Pre mRNA splicing protein, SULFATE ION (2 entities in total) |
| Functional Keywords | c/d guide rna, 2'-o-methylation, coiled-coil, rna binding protein |
| Biological source | Sulfolobus solfataricus |
| Total number of polymer chains | 3 |
| Total formula weight | 87151.14 |
| Authors | |
| 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 Cited by 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: 19666563DOI: 10.1073/pnas.0905128106 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.1 Å) |
Structure validation
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