SNAP output for PDB entry 3s4g [SNAP web server]

PDB-id

3s4g; SNAP-derived features in text and JSON formats; DNAproDB

Class

virus

Method

X-ray (6.0 Å)

Summary

Low resolution structure of stnv complexed with RNA

Reference

Lane SW, Dennis CA, Lane CL, Trinh CH, Rizkallah PJ, Stockley PG, Phillips SE (2011): "Construction and crystal structure of recombinant STNV capsids." J.Mol.Biol., 413, 41-50. doi: 10.1016/j.jmb.2011.07.062.

Abstract

A codon-optimised gene has been expressed in Escherichia coli to produce the coat protein (CP) of the Satellite Tobacco Necrosis Virus. This protein assembles in vivo into capsids closely resembling those of the T=1 wild-type virus. These virus-like particles (VLPs) package the recombinant mRNA transcript and can be disassembled and reassembled using different buffer conditions. The X-ray crystal structure of the VLP has been solved and refined at 1.4 Å resolution and shown to be very similar to that of wild-type Satellite Tobacco Necrosis Virus, except that icosahedral symmetry constraints could be removed to reveal differences between subunits, presumably owing to crystal packing. An additional low-resolution X-ray crystal structure determination revealed well-ordered RNA fragments lodged near the inside surface of the capsid, close to basic clusters formed by the N-terminal helices that project into the interior of the particle. The RNA consists of multiple copies of a 3-bp helical stem, with a single unpaired base at the 3' end, and probably consists of a number of short stem-loops where the loop region is disordered. The arrangement of the RNA is different from that observed in other satellite viruses.