Structure of human Nav1.5 reveals the fast inactivation-related segments as a mutational hotspot for the long QT syndrome

Significance Dysfunction of Nav1.5, the primary cardiac Nav channel, is associated with multiple arrhythmia syndromes, exemplified by type 3 long QT syndrome (LQT3) and Brugada syndrome (BrS). Establishment of the structure-function relationship and mechanistic understanding of the disease variants will facilitate the development of antiarrhythmic drugs. Here we report the cryo-EM structure of human Nav1.5-E1784K, the most common variant shared by LQT3 and BrS. Structural mapping of 91 LQT3-associated mutations reveal a hotspot that involves the fast inactivation segments. The high density of LQT3 mutation sites in this region can be reasonably interpreted by the “door wedge” model for fast inactivation, which was derived from our previous structural observations and is supported by a wealth of functional characterizations. Nav1.5 is the primary voltage-gated Na+ (Nav) channel in the heart. Mutations of Nav1.5 are associated with various cardiac disorders exemplified by the type 3 long QT syndrome (LQT3) and Brugada syndrome (BrS). E1784K is a common mutation that has been found in both LQT3 and BrS patients. Here we present the cryo-EM structure of the human Nav1.5-E1784K variant at an overall resolution of 3.3 Å. The structure is nearly identical to that of the wild-type human Nav1.5 bound to quinidine. Structural mapping of 91- and 178-point mutations that are respectively associated with LQT3 and BrS reveals a unique distribution pattern for LQT3 mutations. Whereas the BrS mutations spread evenly on the structure, LQT3 mutations are clustered mainly to the segments in repeats III and IV that are involved in gating, voltage-sensing, and particularly inactivation. A mutational hotspot involving the fast inactivation segments is identified and can be mechanistically interpreted by our “door wedge” model for fast inactivation. The structural analysis presented here, with a focus on the impact of mutations on inactivation and late sodium current, establishes a structure-function relationship for the mechanistic understanding of Nav1.5 channelopathies.