Visualizing the Nucleotide Addition Cycle of Viral RNA-Dependent RNA Polymerase
AbstractViral RNA-dependent RNA polymerases (RdRPs) are a class of nucleic acid polymerases bearing unique features from global architecture to catalytic mechanisms. In recent years, numerous viral RdRP crystal structures have improved the understanding of these molecular machines, in particular, for how they carry out each nucleotide addition cycle (NAC) as directed by the RNA template. This review focuses on a visual introduction of viral RdRP NAC mechanisms through a combination of static pictures of structural models, a user-friendly software-based assembly of the structural models, and two videos illustrating key conformational changes in the NAC. View Full-Text
- Supplementary File 1:
NAC (ZIP, 8991 KB)This is a PyMOL session file that shows seven viral RdRP NAC reference states (S1, S2, S2-3, S3, S4, S5, S6), five states derived from the reference state by removing the magnesium ions and pyrophosphate (S2m, S2-3m, S3m, S4m, S6m), one norovirus RdRP reference state (nvS3), three movies that connects S2m and S2-3m (closure1), S2-3m and S3m (closure2), S4m and S6m (translocation), and key distance changes during the active site closure (dist01-dist05 for closure1 ; dist06-dist10 for closure2).
- Supplementary File 2:
This is a simplified version of NAC.pse with only the seven reference states included and all hidden atoms deleted from the models, to help reduce the file size for web based PyMOL visualization.
- Supplementary File 3:
Active site closure (MPG, 1320 KB)
- Supplementary File 4:
Translocation (MPG, 1776 KB)
Share & Cite This Article
Wu, J.; Gong, P. Visualizing the Nucleotide Addition Cycle of Viral RNA-Dependent RNA Polymerase. Viruses 2018, 10, 24.
Wu J, Gong P. Visualizing the Nucleotide Addition Cycle of Viral RNA-Dependent RNA Polymerase. Viruses. 2018; 10(1):24.Chicago/Turabian Style
Wu, Jiqin; Gong, Peng. 2018. "Visualizing the Nucleotide Addition Cycle of Viral RNA-Dependent RNA Polymerase." Viruses 10, no. 1: 24.
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