Gating movements and ion permeation in HCN4 pacemaker channels

The HCN1–4 channel family is responsible for the hyperpolarization-activated cation current If/Ih that controls automaticity in cardiac and neuronal pacemaker cells. We present cryoelectron microscopy (cryo-EM) structures of HCN4 in the presence or absence of bound cAMP, displaying the pore domain in closed and open conformations. Analysis of cAMP-bound and -unbound structures sheds light on how ligand-induced transitions in the channel cytosolic portion mediate the effect of cAMP on channel gating and highlights the regulatory role of a Mg2+ coordination site formed between the C-linker and the S4-S5 linker. Comparison of open/closed pore states shows that the cytosolic gate opens through concerted movements of the S5 and S6 transmembrane helices. Furthermore, in combination with molecular dynamics analyses, the open pore structures provide insights into the mechanisms of K+/Na+ permeation. Our results contribute mechanistic understanding on HCN channel gating, cyclic nucleotide-dependent modulation, and ion permeation. [Display omitted] •HCN4 structure is shown in ligand-free and ligand-bound state•Pore domain is shown in closed and in open configuration•Permeability and selectivity mechanisms of HCN channels are uncovered•A metal ion coordination site functionally couples cytoplasmic and transmembrane domains HCN4 channels underlie the pacemaker current that controls heart rate. Saponaro et al. report the structure of HCN4 with the pore in closed and in open configuration and provide information on ion permeability and selectivity. In HCN4, a metal ion coordination site functionally connects the C-linker to the S4-S5 linker.