4PR6: A Second Look at the HDV Ribozyme Structure and Dynamics

Citation:
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.
PDB ID: 4PR6Download
MMDB ID: 124341
PDB Deposition Date: 2014/3/5
Updated in MMDB: 2014/11
Experimental Method:
x-ray diffraction
Resolution: 2.3  Å
Source Organism:
Homo sapiens
Similar Structures:
Biological Unit for 4PR6: dimeric; determined by author and by software (PISA)
Molecular Components in 4PR6
Label Count Molecule
Protein (1 molecule)
1
U1 Small Nuclear Ribonucleoprotein a(Gene symbol: SNRPA)
Molecule annotation
Nucleotide(1 molecule)
1
HDV Ribozyme Self-cleaved
Molecule annotation
Chemicals (16 molecules)
1
16
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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