Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein-RNA complex

Parainfluenza virus 5 (PIV5) is a member of the Paramyxoviridae family of membrane-enveloped viruses with a negative-sense RNA genome that is packaged and protected by long filamentous nucleocapsid-helix structures (RNPs). These RNPs, consisting of ∼2,600 protomers of nucleocapsid (N) protein, form...

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Published in:Proceedings of the National Academy of Sciences - PNAS Vol. 112; no. 14; p. E1792
Main Authors: Alayyoubi, Maher, Leser, George P, Kors, Christopher A, Lamb, Robert A
Format: Journal Article
Language:English
Published: United States 07.04.2015
Subjects:
Binding Sites
Crystallography, X-Ray
Escherichia coli - virology
Microscopy, Electron
Models, Molecular
Nucleoproteins - chemistry
Parainfluenza Virus 5 - chemistry
Protein Binding
Protein Structure, Secondary
Protein Structure, Tertiary
RNA, Viral - chemistry
atomic structure
nucleoprotein
nucleocapsid ring
ribonucleoprotein
paramyxovirus
ISSN:1091-6490, 1091-6490
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Summary:Parainfluenza virus 5 (PIV5) is a member of the Paramyxoviridae family of membrane-enveloped viruses with a negative-sense RNA genome that is packaged and protected by long filamentous nucleocapsid-helix structures (RNPs). These RNPs, consisting of ∼2,600 protomers of nucleocapsid (N) protein, form the template for viral transcription and replication. We have determined the 3D X-ray crystal structure of the nucleoprotein (N)-RNA complex from PIV5 to 3.11-Å resolution. The structure reveals a 13-mer nucleocapsid ring whose diameter, cavity, and pitch/height dimensions agree with EM data from early studies on the Paramyxovirinae subfamily of native RNPs, indicating that it closely represents one-turn in the building block of the RNP helices. The PIV5-N nucleocapsid ring encapsidates a nuclease resistant 78-nt RNA strand in its positively charged groove formed between the N-terminal (NTD) and C-terminal (CTD) domains of its successive N protomers. Six nucleotides precisely are associated with each N protomer, with alternating three-base-in three-base-out conformation. The binding of six nucleotides per protomer is consistent with the "rule of six" that governs the genome packaging of the Paramyxovirinae subfamily of viruses. PIV5-N protomer subdomains are very similar in structure to the previously solved Nipah-N structure, but with a difference in the angle between NTD/CTD at the RNA hinge region. Based on the Nipah-N structure we modeled a PIV5-N open conformation in which the CTD rotates away from the RNA strand into the inner spacious nucleocapsid-ring cavity. This rotation would expose the RNA for the viral polymerase activity without major disruption of the nucleocapsid structure.
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ISSN:1091-6490
1091-6490
DOI:10.1073/pnas.1503941112