Structure of human NaV1.6 channel reveals Na+ selectivity and pore blockade by 4,9-anhydro-tetrodotoxin

  • Nat Commun. 2023 Feb 23;14(1):1030. doi: 10.1038/s41467-023-36766-9.
Yue Li  #  1  2  3 ,  Tian Yuan  #  4  5 ,  Bo Huang  #  6 ,  Feng Zhou  6 ,  Chao Peng  4  5 ,  Xiaojing Li  1  3 ,  Yunlong Qiu  1  3 ,  Bei Yang  1 ,  Yan Zhao  7  8 ,  Zhuo Huang  9  10 ,  Daohua Jiang  11  12
Affiliations
  • 1. National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
  • 2. Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
  • 3. University of Chinese Academy of Sciences, Beijing, 100049, China.
  • 4. State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, 100191, China.
  • 5. IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China.
  • 6. Beijing StoneWise Technology Co Ltd., 15 Haidian Street, Haidian District, Beijing, China.
  • 7. National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [email protected].
  • 8. University of Chinese Academy of Sciences, Beijing, 100049, China. [email protected].
  • 9. State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, 100191, China. [email protected].
  • 10. IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China. [email protected].
  • 11. Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China. [email protected].
  • 12. University of Chinese Academy of Sciences, Beijing, 100049, China. [email protected].
  • # Contributed equally.
PMID: 36823201 DOI: 10.1038/s41467-023-36766-9
Abstract

The Sodium Channel NaV1.6 is widely expressed in neurons of the central and peripheral nervous systems, which plays a critical role in regulating neuronal excitability. Dysfunction of NaV1.6 has been linked to epileptic encephalopathy, intellectual disability and movement disorders. Here we present cryo-EM structures of human NaV1.6/β1/β2 alone and complexed with a guanidinium neurotoxin 4,9-anhydro-tetrodotoxin (4,9-ah-TTX), revealing molecular mechanism of NaV1.6 inhibition by the blocker. The apo-form structure reveals two potential Na+ binding sites within the selectivity filter, suggesting a possible mechanism for Na+ selectivity and conductance. In the 4,9-ah-TTX bound structure, 4,9-ah-TTX binds to a pocket similar to the tetrodotoxin (TTX) binding site, which occupies the Na+ binding sites and completely blocks the channel. Molecular dynamics simulation results show that subtle conformational differences in the selectivity filter affect the affinity of TTX analogues. Taken together, our results provide important insights into NaV1.6 structure, ion conductance, and inhibition.