4PDB
CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS RIBOSOMAL PROTEIN S8 IN COMPLEX WITH AN RNA APTAMER
Summary for 4PDB
| Entry DOI | 10.2210/pdb4pdb/pdb |
| Related | 2LUN |
| Descriptor | 30S ribosomal protein S8, SELEX RNA aptamer (3 entities in total) |
| Functional Keywords | protein-rna complex selex base triple translation, ribosomal protein-rna complex, ribosomal protein/rna |
| Biological source | Bacillus anthracis More |
| Total number of polymer chains | 2 |
| Total formula weight | 29576.45 |
| Authors | Davlieva, M.,Shamoo, Y.,Nikonowicz, E.P. (deposition date: 2014-04-17, release date: 2014-09-03, Last modification date: 2023-12-27) |
| Primary citation | Davlieva, M.,Donarski, J.,Wang, J.,Shamoo, Y.,Nikonowicz, E.P. Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis. Nucleic Acids Res., 42:10795-10808, 2014 Cited by PubMed Abstract: Several protein-targeted RNA aptamers have been identified for a variety of applications and although the affinities of numerous protein-aptamer complexes have been determined, the structural details of these complexes have not been widely explored. We examined the structural accommodation of an RNA aptamer that binds bacterial r-protein S8. The core of the primary binding site for S8 on helix 21 of 16S rRNA contains a pair of conserved base triples that mold the sugar-phosphate backbone to S8. The aptamer, which does not contain the conserved sequence motif, is specific for the rRNA binding site of S8. The protein-free RNA aptamer adopts a helical structure with multiple non-canonical base pairs. Surprisingly, binding of S8 leads to a dramatic change in the RNA conformation that restores the signature S8 recognition fold through a novel combination of nucleobase interactions. Nucleotides within the non-canonical core rearrange to create a G-(G-C) triple and a U-(A-U)-U quartet. Although native-like S8-RNA interactions are present in the aptamer-S8 complex, the topology of the aptamer RNA differs from that of the helix 21-S8 complex. This is the first example of an RNA aptamer that adopts substantially different secondary structures in the free and protein-bound states and highlights the remarkable plasticity of RNA secondary structure. PubMed: 25140011DOI: 10.1093/nar/gku743 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.6 Å) |
Structure validation
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