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3DD2

Crystal structure of an RNA aptamer bound to human thrombin

Summary for 3DD2
Entry DOI10.2210/pdb3dd2/pdb
Related PRD IDPRD_000020
DescriptorThrombin light chain, Thrombin heavy chain, RNA (26-MER), ... (9 entities in total)
Functional Keywordsthrombin, aptamer, rna, dna, heparin, exosite, protease, serine protease, hydrolase-hydrolase inhibitor-rna complex, hydrolase/hydrolase inhibitor/rna
Biological sourceHomo sapiens (human)
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Cellular locationSecreted, extracellular space: P00734 P00734
Total number of polymer chains3
Total formula weight42973.57
Authors
Long, S.B.,Sullenger, B.A. (deposition date: 2008-06-04, release date: 2008-11-11, Last modification date: 2023-08-30)
Primary citationLong, 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: 18971322
DOI: 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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