8QKM

Symmetric structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 gRNA

Summary for 8QKM

• Entry DOI: 10.2210/pdb8qkm/pdb
• EMDB information: 18466
• Descriptor: Capsid protein, CALCIUM ION (2 entities in total)
• Functional Keywords: stnv, cryoem, virus like particle
• Biological source: Satellite tobacco necrosis virus 1
• Total number of polymer chains: 60
• Total formula weight: 1249679.04

Authors

Javed, A.,Mata, P.C.,Stockley, P. (deposition date: 2023-09-15, release date: 2025-03-26, Last modification date: 2025-10-08)

Primary citation

Wroblewski, E.,Patel, N.,Javed, A.,Mata, C.P.,Chandler-Bostock, R.,Lekshmi, B.G.,Ulamec, S.M.,Clark, S.,Phillips, S.E.V.,Ranson, N.A.,Twarock, R.,Stockley, P.G.
Visualizing Viral RNA Packaging Signals in Action.
J.Mol.Biol., 436:168765-168765, 2024

PubMed Abstract: Here we confirm, using genome-scale RNA fragments in assembly competition assays, that multiple sub-sites (Packaging Signals, PSs) across the 5' two-thirds of the gRNA of Satellite Tobacco Necrosis Virus-1 make sequence-specific contacts to the viral CPs helping to nucleate formation of its T = 1 virus-like particle (VLP). These contacts explain why natural virions only package their positive-sense genomes. Asymmetric cryo-EM reconstructions of these VLPs suggest that interactions occur between amino acid residues in the N-terminal ends of the CP subunits and the gRNA PS loop sequences. The base-paired stems of PSs also act non-sequence-specifically by electrostatically promoting the assembly of CP trimers. Importantly, alterations in PS-CP affinity result in an asymmetric distribution of bound PSs inside VLPs, with fuller occupation of the higher affinity 5' PS RNAs around one vertex, decreasing to an RNA-free opposite vertex within the VLP shell. This distribution suggests that gRNA folding regulates cytoplasmic genome extrusion so that the weakly bound 3' end of the gRNA, containing the RNA polymerase binding site, extrudes first. This probably occurs after cation-loss induced swelling of the CP-shell, weakening contacts between CP subunits. These data reveal for the first time in any virus how differential PS folding propensity and CP affinities support the multiple roles genomes play in virion assembly and infection. The high degree of conservation between the CP fold of STNV-1 and those of the CPs of many other viruses suggests that these aspects of genome function will be widely shared.

PubMed: 39214281
DOI: 10.1016/j.jmb.2024.168765

Experimental method

ELECTRON MICROSCOPY (2.39 Å)