2JWV
Structure of a high affinity anti-NFkB RNA aptamer
Summary for 2JWV
| Entry DOI | 10.2210/pdb2jwv/pdb |
| Related | 1OOA |
| NMR Information | BMRB: 15538 |
| Descriptor | RNA (29-MER) (1 entity in total) |
| Functional Keywords | rna, asymmetric internal bulge, stem loop |
| Total number of polymer chains | 1 |
| Total formula weight | 9326.56 |
| Authors | Reiter, N.J.,Maher III, L.,Butcher, S.E. (deposition date: 2007-10-25, release date: 2008-01-08, Last modification date: 2024-05-01) |
| Primary citation | Reiter, N.J.,Maher, L.J.,Butcher, S.E. DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer Nucleic Acids Res., 36:1227-1236, 2008 Cited by PubMed Abstract: The binding of RNA molecules to proteins or other ligands can require extensive RNA folding to create an induced fit. Understanding the generality of this principle involves comparing structures of RNA before and after complex formation. Here we report the NMR solution structure of a 29-nt RNA aptamer whose crystal structure had previously been determined in complex with its transcription factor target, the p50(2) form of NF-kappaB. The RNA aptamer internal loop structure has pre-organized features that are also found in the complex, including non-canonical base pairing and cross-strand base stacking. Remarkably, the free RNA aptamer structure possesses a major groove that more closely resembles B-form DNA than RNA. Upon protein binding, changes in RNA structure include the kinking of the internal loop and distortion of the terminal tetraloop. Thus, complex formation involves both pre-formed and induced fit binding interactions. The high affinity of the NF-kappaB transcription factor for this RNA aptamer may largely be due to the structural pre-organization of the RNA that results in its ability to mimic DNA. PubMed: 18160411DOI: 10.1093/nar/gkm1141 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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