View source for 8qkp


==Asymmetric structure of Satellite Tobacco Necrosis Virus-Like Particle with PS2/3 gRNA==
<StructureSection load='8qkp' size='340' side='right'caption='[[8qkp]], [[Resolution|resolution]] 5.26&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8qkp]] is a 60 chain structure with sequence from [https://en.wikipedia.org/wiki/Satellite_tobacco_necrosis_virus_1 Satellite tobacco necrosis virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8QKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8QKP FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 5.26&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SRA:ADENOSINE+-5-THIO-MONOPHOSPHATE'>SRA</scene>, <scene name='pdbligand=SSU:URIDINE-5-PHOSPHOROTHIOATE'>SSU</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8qkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8qkp OCA], [https://pdbe.org/8qkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8qkp RCSB], [https://www.ebi.ac.uk/pdbsum/8qkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8qkp ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CAPSD_STNV1 CAPSD_STNV1] Self-assembles to form an icosahedral capsid of 17 nm in diameter.<ref>PMID:21839089</ref> <ref>PMID:23318955</ref> <ref>PMID:6481804</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.

Visualizing Viral RNA Packaging Signals in Action.,Wroblewski E, Patel N, Javed A, Mata CP, Chandler-Bostock R, Lekshmi BG, Ulamec SM, Clark S, Phillips SEV, Ranson NA, Twarock R, Stockley PG J Mol Biol. 2024 Nov 15;436(22):168765. doi: 10.1016/j.jmb.2024.168765. Epub 2024 , Aug 29. PMID:39214281<ref>PMID:39214281</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8qkp" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Satellite tobacco necrosis virus 1]]
[[Category: Javed A]]
[[Category: Mata PC]]
[[Category: Stockley P]]