Cryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by {alpha}-amanitin [Protein Structure and Folding] (Journal of Biological Chemistry)

RNA polymerase II (Pol II) is the central enzyme that transcribes eukaryotic protein-coding genes to produce mRNA. The mushroom toxin ?-amanitin binds Pol II and inhibits transcription at the step of RNA chain elongation. Pol II from yeast binds ?-amanitin with micromolar affinity, whereas metazoan Pol II enzymes exhibit nanomolar affinities. Here, we present the high-resolution cryo-EM structure of ?-amanitin bound to and inhibited by its natural target, the mammalian Pol II elongation complex. The structure revealed that the toxin is located in a pocket previously identified in yeast Pol II but forms additional contacts with metazoan-specific residues, which explains why its affinity to mammalian Pol II is ~3000 times higher than for yeast Pol II. Our work provides the structural basis for the inhibition of mammalian Pol II by the natural toxin ?-amanitin and highlights that cryo-EM is well suited to studying interactions of a small molecule with its macromolecular target.