4XJN image
Deposition Date 2015-01-08
Release Date 2015-03-18
Last Version Date 2024-11-06
Entry Detail
PDB ID:
4XJN
Title:
Structure of the parainfluenza virus 5 nucleocapsid-RNA complex: an insight into paramyxovirus polymerase activity
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.11 Å
R-Value Free:
0.26
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Nucleocapsid
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L, M
Chain Length:525
Number of Molecules:13
Biological Source:Parainfluenza virus 5
Polymer Type:polyribonucleotide
Molecule:RNA (78-MER)
Chain IDs:N
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli
Ligand Molecules
Primary Citation
Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein-RNA complex.
Proc.Natl.Acad.Sci.USA 112 E1792 E1799 (2015)
PMID: 25831513 DOI: 10.1073/pnas.1503941112

Abstact

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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