Highlights d HCN4 structure is shown in ligand-free and ligandbound state d Pore domain is shown in closed and in open configuration d Permeability and selectivity mechanisms of HCN channels are uncovered d A metal ion coordination site functionally couples cytoplasmic and transmembrane domains

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Highlights d HCN4 structure is shown in ligand-free and ligandbound state d Pore domain is shown in closed and in open configuration d Permeability and selectivity mechanisms of HCN channels are uncovered d A metal ion coordination site functionally couples cytoplasmic and transmembrane domains

Hyperpolarization-activated cyclic-nucleotide gated (HCN) channels are important for timing biological processes like heartbeat and neuronal firing. Their weak cation selectivity is determined by a filter domain with only two binding sites for K+ and one for Na+. The latter acts as a weak blocker, which is released in combination with a dynamic widening of the filter by K+ ions, giving rise to a mixed K+/Na+ current. Here, we apply molecular dynamics simulations to systematically investigate the interactions of five alkali metal cations with the filter of the open HCN4 pore. Simulations recapitulate experimental data like a low Li+ permeability, considerable Rb+ conductance, a block by Cs+ as well as a punch through of Cs+ ions at high negative voltages. Differential binding of the cation species in specific filter sites is associated with structural adaptations of filter residues. This gives rise to ion coordination by a cation-characteristic number of oxygen atoms from the filter backbone and solvent. This ion/protein interplay prevents Li+, but not Na+, from entry into and further passage through the filter. The site equivalent to S3 in K+ channels emerges as a preferential binding and presumably blocking site for Cs+. Collectively, the data suggest that the weak cation selectivity of HCN channels and their block by Cs+ are determined by restrained cation-generated rearrangements of flexible filter residues.

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