4XJN

Structure of the parainfluenza virus 5 nucleocapsid-RNA complex: an insight into paramyxovirus polymerase activity

Summary for 4XJN

• Entry DOI: 10.2210/pdb4xjn/pdb
• Descriptor: Nucleocapsid, RNA (78-MER), LEAD (II) ION (3 entities in total)
• Functional Keywords: piv5, nucleocapsid, rna, complex, viral protein-rna complex, viral protein/rna
• Biological source: Parainfluenza virus 5; More
• Cellular location: Virion : W5QKM4
• Total number of polymer chains: 14
• Total formula weight: 785923.84

Authors

Alayyoubi, M.,Leser, G.P.,Kors, C.A.,Lamb, R.A. (deposition date: 2015-01-08, release date: 2015-03-18, Last modification date: 2024-11-06)

Primary citation

Alayyoubi, M.,Leser, G.P.,Kors, C.A.,Lamb, R.A.
Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein-RNA complex.
Proc.Natl.Acad.Sci.USA, 112:E1792-E1799, 2015

PubMed Abstract: 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.

PubMed: 25831513
DOI: 10.1073/pnas.1503941112

Experimental method

X-RAY DIFFRACTION (3.11 Å)