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Structural basis for CaVα2δ:gabapentin binding

Nature Structural & Molecular Biology volume 30, pages 735–739 (2023)Cite this article

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Abstract

Gabapentinoid drugs for pain and anxiety act on the CaVα2δ-1 and CaVα2δ-2 subunits of high-voltage-activated calcium channels (CaV1s and CaV2s). Here we present the cryo-EM structure of the gabapentin-bound brain and cardiac CaV1.2/CaVβ3/CaVα2δ-1 channel. The data reveal a binding pocket in the CaVα2δ-1 dCache1 domain that completely encapsulates gabapentin and define CaVα2δ isoform sequence variations that explain the gabapentin binding selectivity of CaVα2δ-1 and CaVα2δ-2.

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Fig. 1: Structure of the CaV1.2(ΔC)/CaVβ3/Cavα2δ-1:GBP complex.
Fig. 2: Comparison of CaVα2δ-1 GBP-binding sites.

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Data availability

Cav1.2(ΔC)/Cavβ3/Cavα2δ-1:GBP coordinates and maps (PDB 8FD7, EMD-29004, EMD-29007 and EMD-29015) and the map of the EMC:Cav1.2(ΔC)/Cavβ3 complex (EMD-29006) are deposited with the RCSB and EMDB. Requests for materials should be addressed to D.L.M.

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Acknowledgements

We thank D. Bulkley for technical help and K. Brejc for comments on the manuscript. This work was supported by grant no. NIH R01 HL080050 to D.L.M.

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Author notes

  1. These authors contributed equally: Zhou Chen, Abhisek Mondal.

Authors and Affiliations

  1. Cardiovascular Research Institute, University of California, San Francisco, CA, USA

    Zhou Chen, Abhisek Mondal & Daniel L. Minor Jr

  2. Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA

    Daniel L. Minor Jr

  3. California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA, USA

    Daniel L. Minor Jr

  4. Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA, USA

    Daniel L. Minor Jr

  5. Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Daniel L. Minor Jr

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Contributions

Z.C., A.M. and D.L.M. conceived the study and designed the experiments. Z.C. expressed and characterized the samples. Z.C. and A.M. collected and analyzed the cryo-EM data. Z.C. and A.M. built and refined the atomic models. D.L.M. analyzed data and provided guidance and support. Z.C., A.M. and D.L.M. wrote the paper.

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Correspondence to Daniel L. Minor Jr.

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The authors declare no competing interests.

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Nature Structural & Molecular Biology thanks Rachelle Gaudet and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Katarzyna Ciazynska, in collaboration with the Nature Structural & Molecular Biology team. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 CaV1.2(ΔC)/CaVβ3/CaVα2δ-1:GBP Cryo-EM analysis.

a, Exemplar CaV1.2(ΔC)/CaVβ3/CaVα2δ-1:GBP electron micrograph (~105,000x magnification) and 2D class averages. N = 3. b, Workflow for electron microscopy data processing for CaV1.2(ΔC)/CaVβ3/CaVα2δ-1:GBP sample. Initial cryoSPARC-3.2 Ab initio reconstruction identified a population of particles containing the CaV1.2(ΔC)/CaVβ3/CaVα2δ-1 and EMC:CaV1.2(ΔC)/CaVβ3 complexes, similar to prior studies13. Red arrows indicate the two classes that were re-extracted, subjected to multiple rounds of 3D heterogeneous classification, and exported from cryoSPARC-3.2 for further 3D refinement in RELION-3.1. Particle subtraction was performed for both the refined maps in Relion-3.1 followed by 3D classification with single class and 3D refinement to get the final consensus maps. Multibody refinement was performed to enhance features of CaVα2δ-1, which was used for the CaV1.2(ΔC)/CaVβ3/CaVα2δ-1:GBP composite map. The composite map was used for model building and refinement.

Extended Data Fig. 2 CaV1.2(ΔC)/CaV β3/CaVα2δ-1:GBP map and model quality.

a, Particle distribution plot and gold-standard Fourier shell correlation (FSC) curve for the overall CaV1.2(ΔC)/CaV β3/CaVα2δ-1:GBP complex map and the extracellular map containing CaVα2δ-1:GBP. b, local resolution for the overall CaV1.2(ΔC)/CaV β3/CaVα2δ-1:GBP map and the extracellular map containing CaVα2δ-1:GBP. c, local B-factor for the overall CaV1.2(ΔC)/CaV β3/CaVα2δ-1:GBP model and the CaVα2δ-1:GBP subunit. d, Particle distribution plot and gold-standard Fourier shell correlation (FSC) curve for the EMC:CaV1.2(ΔC)/CaVβ3 complex from the CaV1.2(ΔC)/CaV β3/CaVα2δ-1:GBP sample. e, EMC:CaV1.2(ΔC)/CaVβ3 complex local resolution. Select elements of each complex are labeled.

Extended Data Fig. 3 CaV1.2(ΔC)/CaVβ3/CaVα2δ-1:GBP Cryo-EM maps.

a, CaV1.2(ΔC)/CaVβ3/CaVα2δ-1 side view (left) and extracellular (right) view. Subunits are colored: CaV1.2 (slate) and CaVβ3 (violet). CaVα2δ domains are colored as: dCache1 (aquamarine), dCache2 (orange), VWA:MIDAS (green), and CaVδ (yellow). Grey bars denote the membrane. b-e, CaVα2δ-1 subdomain representative maps for b, VWA:MIDAS domain, c, dCache1, d, dCache2:CaVδ. Part of CaVδ completes the second β-barrel subdomain of dCache2, e, CaVδ. f, GBP-binding site. Maps are rendered at 9–10σ. Domain colors are as in a.

Extended Data Fig. 4 CaVα2δ-1 GBP-binding site analysis and comparisons.

a, Superposition of the CaVα2δ-1:GBP (aquamarine) and CaVα2δ-1:L-Leu (orange) (PDB:8EOG)13 binding sites. GBP is red. L-Leu is purple. b and c, LigPLOT37 diagrams of the b, CaVα2δ-1:GBP (aquamarine) and c, CaVα2δ-1:L-Leu (orange) (PDB:8EOG)13 binding sites showing hydrogen bonds and ionic interactions (dashed lines) and van der Waals contacts ≤ 5 Å. GBP is red. L-Leu is purple. d, Superposition of the first dCache1 repeats from CaVα2δ-1:GBP (aquamarine) and the PctA:L-Ile complex (magenta) (PDB: 5T65)34. GBP is red. e,f, Closeup view of superposition from ‘d’ showing ligand contact residues. CaVα2δ-1 is shown as a cartoon. GBP is red. Corresponding sidechains of PctA are magenta. L-Ile form the PctA complex is pink. PctA residues are labeled in italics.

Supplementary information

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Supplementary Video 1

CaVα2δ-1 ligand binding site cryo-EM density comparison. Video shows superposition of maps for the CaVα2δ-1:GBP (13.9σ; clear) and CaVα2δ-1:L-Leu (7.5σ; orange) (EMD-28375)13, GBP (red) and L-Leu (purple) are shown as sticks.

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Chen, Z., Mondal, A. & Minor, D.L. Structural basis for CaVα2δ:gabapentin binding. Nat Struct Mol Biol 30, 735–739 (2023). https://doi.org/10.1038/s41594-023-00951-7

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