Here we test the role of the CLZ domain by measuring the subunit composition of CNGA1 + CNGB1 channels when the CLZ domain in the CNGA1 subunit was deleted. Using electrophysiology and fluorescence measurements, we found that deletion of the CLZ domain relaxed the constrained subunit stoichiometry. This allowed more than one CNGB1 subunit in the channel and conferred novel pharmacological properties and cyclic nucleotide specificity. Using X-ray crystallography, we found that the CLZ domains of both CNGA1 and CNGA3 formed homotypic parallel 3-helix coiled-coil domains, consistent with their proposed role in regulating subunit assembly.