SNAP output for PDB entry 1pgl [SNAP web server]

PDB-id

1pgl; SNAP-derived features in text and JSON formats; DNAproDB

Class

virus-RNA

Method

X-ray (2.8 Å)

Summary

Bean pod mottle virus (bpmv), middle component

Reference

Lin T, Cavarelli J, Johnson JE (2003): "Evidence for assembly-dependent folding of protein and RNA in an icosahedral virus." Virology, 314, 26-33. doi: 10.1016/S0042-6822(03)00457-4.

Abstract

Ordered nucleic acid in an icosahedral virus was first visualized in the X-ray structure of the Picorna-like plant virus, Bean pod mottle virus (BPMV). Virus particles containing the 3500 nucleotide segment of the BPMV bipartite RNA genome (middle component) had nearly 20% of the genome ordered. Here we report the refined structures of the middle component, bottom component (particles containing the 5800 nucleotide segment of the genome), and top component (empty particles of BPMV capsid protein). The bottom component particles contain ordered RNA in the same location as middle component. Although the ordered RNA density in both nucleoprotein particles is the average of the contents of 60 icosahedral asymmetric units, both nucleoprotein components show that the base density for the first two nucleotides is predominantly purine, while the next five appear to be predominantly pyrimidine. The empty capsid demonstrates that RNA dictates the order of the N-terminal 19 residues of the large subunit because these residues are invisible in the top component.