3DD2
Crystal structure of an RNA aptamer bound to human thrombin
Summary for 3DD2
| Entry DOI | 10.2210/pdb3dd2/pdb |
| Related PRD ID | PRD_000020 |
| Descriptor | Thrombin light chain, Thrombin heavy chain, RNA (26-MER), ... (9 entities in total) |
| Functional Keywords | thrombin, aptamer, rna, dna, heparin, exosite, protease, serine protease, hydrolase-hydrolase inhibitor-rna complex, hydrolase/hydrolase inhibitor/rna |
| Biological source | Homo sapiens (human) More |
| Cellular location | Secreted, extracellular space: P00734 P00734 |
| Total number of polymer chains | 3 |
| Total formula weight | 42973.57 |
| Authors | Long, S.B.,Sullenger, B.A. (deposition date: 2008-06-04, release date: 2008-11-11, Last modification date: 2024-11-20) |
| Primary citation | Long, S.B.,Long, M.B.,White, R.R.,Sullenger, B.A. Crystal structure of an RNA aptamer bound to thrombin. Rna, 14:2504-2512, 2008 Cited by PubMed Abstract: Aptamers, an emerging class of therapeutics, are DNA or RNA molecules that are selected to bind molecular targets that range from small organic compounds to large proteins. All of the determined structures of aptamers in complex with small molecule targets show that aptamers cage such ligands. In structures of aptamers in complex with proteins that naturally bind nucleic acid, the aptamers occupy the nucleic acid binding site and often mimic the natural interactions. Here we present a crystal structure of an RNA aptamer bound to human thrombin, a protein that does not naturally bind nucleic acid, at 1.9 A resolution. The aptamer, which adheres to thrombin at the binding site for heparin, presents an extended molecular surface that is complementary to the protein. Protein recognition involves the stacking of single-stranded adenine bases at the core of the tertiary fold with arginine side chains. These results exemplify how RNA aptamers can fold into intricate conformations that allow them to interact closely with extended surfaces on non-RNA binding proteins. PubMed: 18971322DOI: 10.1261/rna.1239308 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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