Structure
Volume 28, Issue 9, 1 September 2020, Pages 979-990.e4
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Article
Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNA

https://doi.org/10.1016/j.str.2020.07.001Get rights and content
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Highlights

  • HRSV M2-1 is a transcription anti-terminator regulating polymerase processivity

  • Hydrophobic residue Phe23 is indispensable for M2-1 to recognize the base of RNA

  • Zinc-binding domain (ZBD) and core domain (CD) of M2-1 independently interact RNA

  • Dynamic binding of RNA to similar domains of M2-1 is observed in GaMD simulations

Summary

The M2-1 protein of human respiratory syncytial virus (HRSV) is a transcription anti-terminator that regulates the processivity of the HRSV RNA-dependent RNA polymerase (RdRP). Here, we report a crystal structure of HRSV M2-1 bound to a short positive-sense gene-end RNA (SH7) at 2.7 Å resolution. We identified multiple critical residues of M2-1 involved in RNA interaction and examined their roles using mutagenesis and MicroScale Thermophoresis (MST) assay. We found that hydrophobic residue Phe23 is indispensable for M2-1 to recognize the base of RNA. We also captured spontaneous binding of RNA (SH7) to M2-1 in all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method. Both experiments and simulations revealed that the interactions of RNA with two separate domains of M2-1, the zinc-binding domain (ZBD) and the core domain (CD), are independent of each other. Collectively, our results provided a structural basis for RNA recognition by HRSV M2-1.

Keywords

crystal structure
human respiratory syncytial virus
M2-1
RNA
Gaussian accelerated molecular dynamics
microscale thermophoresis assay
simulations
structural basis

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