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Structure of the human cone photoreceptor cyclic nucleotide-gated channel

Nature Structural & Molecular Biology volume 29, pages 40–46 (2022)Cite this article

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Abstract

Cyclic nucleotide-gated (CNG) channels transduce light-induced chemical signals into electrical signals in retinal cone and rod photoreceptors. Structures of native CNG channels, which are heterotetramers formed by CNGA and CNGB subunits, have not been obtained. In the present study, we report a high-resolution cryo-electron microscopy structure of the human cone CNG channel in the apo closed state. The channel contains three CNGA3 and one CNGB3 subunits. Arg403 in the pore helix of CNGB3 projects into an asymmetric selectivity filter and forms hydrogen bonds with two pore-lining backbone carbonyl oxygens. Arg442 in S6 of CNGB3 protrudes into and occludes the pore below the hydrophobic cavity gate previously observed in homotetrameric CNGA channels. It is interesting that Arg403Gln is a disease mutation, and Arg442 is replaced by glutamine in some animal species with dichromatic or monochromatic vision. These and other unique structural features and the disease link conferred by CNGB3 indicate a critical role of CNGB3 in shaping cone photoresponses.

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Fig. 1: Cryo-EM structure of apo human A3/B3.
Fig. 2: Comparison of A3 and B3 structures.
Fig. 3: The ion conduction pathway.
Fig. 4: The cavity gate and inner gate.
Fig. 5: The SF.
Fig. 6: The C-linker and CNBD.

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Data availability

The authors declare that the data supporting the findings of the present study are available within the paper. The cryo-EM density map has been deposited in the Electron Microscopy Data Bank under accession no. EMD-24468. The coordinates of the atomic model have been deposited in the PDB under accession no. 7RHS. Several structural coordinates in the PDB database were used in the present study, which can be located under accession nos. 6WEJ and 7LFT. Source data are provided with this paper.

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Acknowledgements

This research was supported by the National Institutes of Health (NIH) (grant nos. RO1EY027800 and RO1GM085234 to J.Y.). Some of this work was performed at the Columbia University Cryo-Electron Microscopy Center (CUCEC) and the Simons Electron Microscopy Center and National Resource for Automated Molecular Microscopy located at New York Structural Biology Center (NYSBC), supported by grants from the Simons Foundation (grant no. SF349247), NYSTAR and the NIH National Institute of General Medical Sciences (grant no. GM103310) with additional support from Agouron Institute (grant no. F00316) and NIH (grant no. OD019994). Some cryo-EM work was performed at the National Center for CryoEM Access and Training (NCCAT), supported by the NIH Common Fund Transformative High Resolution Cryo-Electron Microscopy program (U24 GM129539). We thank members of CUCEC, NYSBC and NCCAT for support and assistance in cryo-EM grid screening and data acquisition. We thank members of our laboratory for discussion during the course of this work.

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  1. Department of Biological Sciences, Columbia University, New York, NY, USA

    Xiangdong Zheng, Zhengshan Hu, Huan Li & Jian Yang

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  1. Xiangdong Zheng
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Contributions

X.Z. and J.Y. conceived the project. X.Z. designed and performed biochemical and cryo-EM experiments, built the atomic models and analyzed the results. Z.H. and H.L. performed and analyzed the liposome recordings. J.Y. analyzed the results and wrote the paper with X.Z. and Z.H.

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Correspondence to Jian Yang.

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Extended data

Extended Data Fig. 1 Cryo-EM single-particle analysis of apo A3/B3.

a, Gel filtration profile of heterotetrameric A3/B3 sample. b, SDS-PAGE of A3/B3 sample used for cryo-EM. c, A representative motion-corrected micrograph. Scale bar: 100 nm. d, Gallery of typical averages from 2D classification. e, Flow chart of cryo-EM image processing. f, FSC curve of the final 3D reconstructions. FSC threshold: 0.143. g, Euler angle distribution of particles used in the final 3D reconstruction. h, Local resolution of the final density map. i, FSC curves for cross-validation between maps and model. Black, model versus the summed map. Blue, model versus the half map that was used for model refinement (called ‘work’). Red, model versus another half map that was not used for model refinement (called ‘free’). FSC threshold: 0.143. Uncropped image for panel b is available as source data.

Source data

Extended Data Fig. 2 Cryo-EM density maps and fitting of atomic models of selected key regions in all four subunits of A3/B3.

All maps were low-pass filtered to 2.93 Å, sharpened with a temperature factor of −103 Å2 and contoured at 4σ. NAG: N-acetyl-beta-D-glucosamine.

Extended Data Fig. 3 Liposome recordings of purified A3/B3 channel proteins.

a, Single-channel currents of purified A3/B3 activated by 10 µM cGMP. A total of 29 patches were recorded. Of them, 17 showed no cGMP activity and 12 showed cGMP-activated activity. b, Continuous trace of A3/B3 single-channel current showing inhibition by L-cis-diltiazem (DTZ). c, Amplitude histogram of cGMP-induced currents at + 80 mV from one patch. d, Single-channel conductance of cGMP-induced currents. Data were presented as mean ± SD. e, Continuous trace of the same patch as in (b) showing a preference of cGMP over cAMP. f, Single-channel open probability of currents evoked by 10 μM cGMP or 10 μM cAMP. Data were presented as mean ± SD.

Source data

Extended Data Fig. 4 Alternative projections of F392 in S6 of A3I.

a, b, Close-up view of F392 in S6 of A3I from the extracellular side (a) and parallel to the membrane (b). Cryo-EM densities are shown as blue mesh and are contoured at 3σ. The dash line marks the pore axis.

Extended Data Fig. 5 Interactions between A’B’ and C’D’ helices of the gating ring.

Side-chains of residues involved in A’B’/C’D’ interactions between A3I and A3II (a), A3II and A3III (b), A3III and B3 (c), and B3 and A3I (d) are shown as sticks. Hydrogen bonds and salt bridges are shown as yellow and purple dash lines, respectively.

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Zheng, X., Hu, Z., Li, H. et al. Structure of the human cone photoreceptor cyclic nucleotide-gated channel. Nat Struct Mol Biol 29, 40–46 (2022). https://doi.org/10.1038/s41594-021-00699-y

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