1NBK
The structure of RNA aptamer for HIV Tat complexed with two argininamide molecules
Summary for 1NBK
| Entry DOI | 10.2210/pdb1nbk/pdb |
| Descriptor | RNA aptamer, 2-AMINO-5-GUANIDINO-PENTANOIC ACID (2 entities in total) |
| Functional Keywords | rna-ligands complex, base triple, rna aptamer, hiv tat, rna |
| Biological source | synthetic construct |
| Total number of polymer chains | 1 |
| Total formula weight | 11271.95 |
| Authors | Matsugami, A.,Kobayashi, S.,Ouhashi, K.,Uesugi, S.,Yamamoto, R.,Taira, K.,Nishikawa, S.,Kumar, P.K.R.,Katahira, M. (deposition date: 2002-12-03, release date: 2003-12-03, Last modification date: 2024-09-18) |
| Primary citation | Matsugami, A.,Kobayashi, S.,Ouhashi, K.,Uesugi, S.,Yamamoto, R.,Taira, K.,Nishikawa, S.,Kumar, P.K.R.,Katahira, M. Structural Basis of the Highly Efficient Trapping of the HIV Tat Protein by an RNA Aptamer Structure, 11:533-545, 2003 Cited by PubMed Abstract: An RNA aptamer containing two binding sites exhibits extremely high affinity to the HIV Tat protein. We have determined the structure of the aptamer complexed with two argininamide molecules. Two adjacent U:A:U base triples were formed, which widens the major groove to make space for the two argininamide molecules. The argininamide molecules bind to the G bases through hydrogen bonds. The binding is stabilized through stacking interactions. The structure of the aptamer complexed with a Tat-derived arginine-rich peptide was also characterized. It was suggested that the aptamer structure is similar for both complexes and that the aptamer interacts with two different arginine residues of the peptide simultaneously at the two binding sites, which could explain the high affinity to Tat. PubMed: 12737819DOI: 10.1016/S0969-2126(03)00069-8 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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