4NWW

Crystal structure of an N-terminally truncated capsid protein mutant of Orsay virus

Summary for 4NWW

• Entry DOI: 10.2210/pdb4nww/pdb
• Related: 4NWV
• Descriptor: Capsid protein, CALCIUM ION (2 entities in total)
• Functional Keywords: beta barrel, virus
• Biological source: Orsay nodavirus
• Total number of polymer chains: 3
• Total formula weight: 118315.00

Authors

Tao, Y.J.,Guo, Y.R. (deposition date: 2013-12-06, release date: 2014-08-20, Last modification date: 2024-11-20)

Primary citation

Guo, Y.R.,Hryc, C.F.,Jakana, J.,Jiang, H.,Wang, D.,Chiu, W.,Zhong, W.,Tao, Y.J.
Crystal structure of a nematode-infecting virus.
Proc.Natl.Acad.Sci.USA, 111:12781-12786, 2014

PubMed 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-δ 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, β-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.

PubMed: 25136116
DOI: 10.1073/pnas.1407122111

Experimental method

X-RAY DIFFRACTION (3.75 Å)