5GIN
Crystal structure of box C/D RNP with 12 nt guide regions and 9 nt substrates
Summary for 5GIN
| Entry DOI | 10.2210/pdb5gin/pdb |
| Related | 5GIO 5GIP |
| Descriptor | C/D box methylation guide ribonucleoprotein complex aNOP56 subunit, 50S ribosomal protein L7Ae, Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase, ... (6 entities in total) |
| Functional Keywords | 2'-o-methylation, guide rna, rnp, transferase-rna complex, transferase/rna |
| Biological source | Sulfolobus solfataricus More |
| Cellular location | Cytoplasm : A0A0E3JZF7 |
| Total number of polymer chains | 15 |
| Total formula weight | 302376.13 |
| Authors | |
| Primary citation | Yang, Z.,Lin, J.,Ye, K. Box C/D guide RNAs recognize a maximum of 10 nt of substrates Proc.Natl.Acad.Sci.USA, 113:10878-10883, 2016 Cited by PubMed Abstract: Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The spacer regions between boxes C to D' and boxes C' to D contain the guide sequence that can form a stretch of base pairs with substrate RNAs. The lengths of spacer regions and guide-substrate duplexes are variable among C/D RNAs. In a previously determined structure of C/D ribonucleoprotein (RNP), a 12-nt-long spacer forms 10 bp with the substrate. How spacers and guide-substrate duplexes of other lengths are accommodated remains unknown. Here we analyze how the lengths of spacers and guide-substrate duplexes affect the modification activity and determine three structures of C/D RNPs assembled with different spacers and substrates. We show that the guide can only form a duplex of a maximum of 10 bp with the substrate during modification. Slightly shorter duplexes are tolerated, but longer duplexes must be unwound to fit into a capped protein channel for modification. Spacers with <12 nucleotides are defective, mainly because they cannot load the substrate in the active conformation. For spacers with >12 nucleotides, the excessive unpaired sequences near the box C/C' side are looped out. Our results provide insight into the substrate recognition mechanism of C/D RNA and refute the RNA-swapped model for dimeric C/D RNP. PubMed: 27625427DOI: 10.1073/pnas.1604872113 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.308 Å) |
Structure validation
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