6YC4

Crystal structure of the steady-state activated state of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0

Summary for 6YC4

• Entry DOI: 10.2210/pdb6yc4/pdb
• Descriptor: Sodium pumping rhodopsin, (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, EICOSANE, ... (8 entities in total)
• Functional Keywords: rhodopsin, ion pumping, retinal, sodium pump, intermediate state, membrane protein
• Biological source: Dokdonia eikasta
• Total number of polymer chains: 5
• Total formula weight: 174142.85

Authors

Kovalev, K.,Gushchin, I.,Gordeliy, V. (deposition date: 2020-03-18, release date: 2020-04-08, Last modification date: 2024-10-23)

Primary citation

Kovalev, K.,Astashkin, R.,Gushchin, I.,Orekhov, P.,Volkov, D.,Zinovev, E.,Marin, E.,Rulev, M.,Alekseev, A.,Royant, A.,Carpentier, P.,Vaganova, S.,Zabelskii, D.,Baeken, C.,Sergeev, I.,Balandin, T.,Bourenkov, G.,Carpena, X.,Boer, R.,Maliar, N.,Borshchevskiy, V.,Buldt, G.,Bamberg, E.,Gordeliy, V.
Molecular mechanism of light-driven sodium pumping.
Nat Commun, 11:2137-2137, 2020

PubMed Abstract: 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.

PubMed: 32358514
DOI: 10.1038/s41467-020-16032-y

Experimental method

X-RAY DIFFRACTION (2.6 Å)