3DD2

Crystal structure of an RNA aptamer bound to human thrombin

3DD2 の概要

• エントリーDOI: 10.2210/pdb3dd2/pdb
• 関連するBIRD辞書のPRD_ID: PRD_000020
• 分子名称: Thrombin light chain, Thrombin heavy chain, RNA (26-MER), ... (9 entities in total)
• 機能のキーワード: thrombin, aptamer, rna, dna, heparin, exosite, protease, serine protease, hydrolase-hydrolase inhibitor-rna complex, hydrolase/hydrolase inhibitor/rna
• 由来する生物種: Homo sapiens (human); 詳細
• 細胞内の位置: Secreted, extracellular space: P00734 P00734
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 42973.57

構造登録者

Long, S.B.,Sullenger, B.A. (登録日: 2008-06-04, 公開日: 2008-11-11, 最終更新日: 2024-11-20)

主引用文献

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

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

実験手法

X-RAY DIFFRACTION (1.9 Å)