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Journal Articles Nature Communications Year : 2020

Molecular mechanism of light-driven sodium pumping

Dmytro Volkov
  • Function : Author
Egor Zinovev
  • Function : Author
Maksim Rulev
  • Function : Author
Alexey Alekseev
  • Function : Author
Antoine Royant
Dmitrii Zabelskii
  • Function : Author
Christian Baeken
  • Function : Author
Ilya Sergeev
  • Function : Author
Xavier Carpena
  • Function : Author
Roeland Boer
  • Function : Author
Nina Maliar
  • Function : Author


The light-driven sodium-pumping rhodopsin KR2 from Krokinobacter eikastus is the only non-proton cation active transporter with demonstrated potential for optogenetics. However, the existing structural data on KR2 correspond exclusively to its ground state, and show no sodium inside the protein, which hampers the understanding of sodium-pumping mechanism. Here we present crystal structure of the O-intermediate of the physiologically relevant pentameric form of KR2 at the resolution of 2.1 Å, revealing a sodium ion near the retinal Schiff base, coordinated by N112 and D116 of the characteristic NDQ triad. We also obtained crystal structures of D116N and H30A variants, conducted metadynamics simulations and measured pumping activities of putative pathway mutants to demonstrate that sodium release likely proceeds alongside Q78 towards the structural sodium ion bound between KR2 protomers. Our findings highlight the importance of pentameric assembly for sodium pump function, and may be used for rational engineering of enhanced optogenetic tools.
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Dates and versions

hal-02864661 , version 1 (25-11-2020)



Kirill Kovalev, Roman Astashkin, Ivan Gushchin, Philipp Orekhov, Dmytro Volkov, et al.. Molecular mechanism of light-driven sodium pumping. Nature Communications, 2020, 11 (1), pp.2137. ⟨10.1038/s41467-020-16032-y⟩. ⟨hal-02864661⟩
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