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.

人呼吸道合胞病毒 (HRSV) 的 M2-1 蛋白是一种转录抗终止子，可调节 HRSV RNA 依赖性 RNA 聚合酶 (RdRP) 的持续合成能力。在这里，我们报告了 HRSV M2-1 的晶体结构，它以 2.7 Å 的分辨率与短的正义基因末端 RNA (SH7) 结合。我们确定了参与 RNA 相互作用的 M2-1 的多个关键残基，并使用诱变和微量热泳 (MST) 测定检查了它们的作用。我们发现疏水残基 Phe23 对于 M2-1 识别 RNA 碱基是必不可少的。我们还使用强大的高斯加速分子动力学 (GaMD) 方法在全原子模拟中捕获了 RNA (SH7) 与 M2-1 的自发结合。实验和模拟都表明 RNA 与 M2-1 的两个独立结构域的相互作用，锌结合域 (ZBD) 和核心域 (CD) 相互独立。总的来说，我们的结果为 HRSV M2-1 的 RNA 识别提供了结构基础。