8PE4 image
Entry Detail
PDB ID:
8PE4
EMDB ID:
Keywords:
Title:
Capsid structure of the L-A helper virus from native viral communities
Biological Source:
PDB Version:
Deposition Date:
2023-06-13
Release Date:
2024-05-22
Method Details:
Experimental Method:
Resolution:
3.21 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Major capsid protein
Chain IDs:A, B
Chain Length:680
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae virus L-A
Ligand Molecules
Primary Citation
Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts.
Commun Biol 7 557 557 (2024)
PMID: 38730276 DOI: 10.1038/s42003-024-06204-7

Abstact

The high abundance of most viruses in infected host cells benefits their structural characterization. However, endogenous viruses are present in low copy numbers and are therefore challenging to investigate. Here, we retrieve cell extracts enriched with an endogenous virus, the yeast L-A virus. The determined cryo-EM structure discloses capsid-stabilizing cation-π stacking, widespread across viruses and within the Totiviridae, and an interplay of non-covalent interactions from ten distinct capsomere interfaces. The capsid-embedded mRNA decapping active site trench is supported by a constricting movement of two flexible opposite-facing loops. tRNA-loaded polysomes and other biomacromolecules, presumably mRNA, are found in virus proximity within the cell extract. Mature viruses participate in larger viral communities resembling their rare in-cell equivalents in terms of size, composition, and inter-virus distances. Our results collectively describe a 3D-architecture of a viral milieu, opening the door to cell-extract-based high-resolution structural virology.

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