4NWV: Crystal structure of Orsay virus-like particle

Citation:
Abstract
Orsay, the first virus discovered to naturally infect Caenorhabditis elegans or any nematode, has a bipartite, positive-sense RNA genome. Sequence analyses show that Orsay is related to nodaviruses, but molecular characterizations of Orsay reveal several unique features, such as the expression of a capsid-delta fusion protein and the use of an ATG-independent mechanism for translation initiation. Here we report the crystal structure of an Orsay virus-like particle assembled from recombinant capsid protein (CP). Orsay capsid has a T = 3 icosahedral symmetry with 60 trimeric surface spikes. Each CP can be divided into three regions: an N-terminal arm that forms an extended protein interaction network at the capsid interior, an S domain with a jelly-roll, beta-barrel fold forming the continuous capsid, and a P domain that forms surface spike projections. The structure of the Orsay S domain is best aligned to T = 3 plant RNA viruses but exhibits substantial differences compared with the insect-infecting alphanodaviruses, which also lack the P domain in their CPs. The Orsay P domain is remotely related to the P1 domain in calicivirus and hepatitis E virus, suggesting a possible evolutionary relationship. Removing the N-terminal arm produced a slightly expanded capsid with fewer nucleic acids packaged, suggesting that the arm is important for capsid stability and genome packaging. Because C. elegans-Orsay serves as a highly tractable model for studying viral pathogenesis, our results should provide a valuable structural framework for further studies of Orsay replication and infection.
PDB ID: 4NWVDownload
MMDB ID: 122526
PDB Deposition Date: 2013/12/6
Updated in MMDB: 2017/12
Experimental Method:
x-ray diffraction
Resolution: 3.25  Å
Source Organism:
Similar Structures:
Biological Unit for 4NWV: 180-meric
Molecular Components in 4NWV
Label Count Molecule
Proteins (180 molecules)
180
Capsid Protein
Molecule annotation
Chemicals (180 molecules)
1
180
* Click molecule labels to explore molecular sequence information.

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