4PR6

A Second Look at the HDV Ribozyme Structure and Dynamics.

「1CX0」から置き換えられました

4PR6 の概要

• エントリーDOI: 10.2210/pdb4pr6/pdb
• 関連するPDBエントリー: 4PRF
• 分子名称: HDV RIBOZYME SELF-CLEAVED, U1 small nuclear ribonucleoprotein A, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: base sequence, binding sites, catalysis, cloning, molecular, computer graphics, escherichia coli, hepatitis delta virus, models, molecular sequence data, nucleic acid conformation, rna, catalytic, viral, rna-binding proteins, ribonucleoprotein, u1 small nuclear, rna binding protein/rna, rna binding protein-rna complex
• 由来する生物種: Homo sapiens (human); 詳細
• 細胞内の位置: Nucleus: P09012
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 57961.83

構造登録者

Kapral, G.J.,Jain, S.,Noeske, J.,Doudna, J.A.,Richardson, D.C.,Richardson, J.S. (登録日: 2014-03-05, 公開日: 2014-10-29, 最終更新日: 2024-11-06)

主引用文献

Kapral, G.J.,Jain, S.,Noeske, J.,Doudna, J.A.,Richardson, D.C.,Richardson, J.S.
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
Nucleic Acids Res., 42:12833-12846, 2014

PubMed Abstract: The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.

PubMed: 25326328
DOI: 10.1093/nar/gku992

実験手法

X-RAY DIFFRACTION (2.3 Å)