Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Crystal structure of a nematode-infecting virus.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 111, Issue 35, Page 12781-12786, Year 2014
Publish date	Sep 2, 2014
Authors	Yusong R Guo / Corey F Hryc / Joanita Jakana / Hongbing Jiang / David Wang / Wah Chiu / Weiwei Zhong / Yizhi J Tao /
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, ...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.
External links	Proc Natl Acad Sci U S A / PubMed:25136116 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	3.25 - 6.9 Å
Structure data	EMDB-5952: CryoEM reconstruction model of Orsay virus-like particle Method: EM (single particle) / Resolution: 6.9 Å PDB-4nwv: Crystal structure of Orsay virus-like particle Method: X-RAY DIFFRACTION / Resolution: 3.25 Å PDB-4nww: Crystal structure of an N-terminally truncated capsid protein mutant of Orsay virus Method: X-RAY DIFFRACTION / Resolution: 3.75 Å
Chemicals	ChemComp-CA: Unknown entry
Source	orsay virus orsay nodavirus
Keywords	VIRUS / beta barrel