6yby | pdb_00006yby

Crystal structure of the D116N mutant of the light-driven sodium pump KR2 in the monomeric form, pH 4.6

spinqualitylabelsall models 6yby, resolution 1.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6yby is a 1 chain structure with sequence from Dokdonia eikasta. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.8Å Ligands: LFA, NA, RET Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function N0DKS8_9FLAO Publication Abstract from PubMed 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 A, 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. Molecular mechanism of light-driven sodium pumping.,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 Nat Commun. 2020 May 1;11(1):2137. doi: 10.1038/s41467-020-16032-y. PMID:32358514 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Rhodopsin 3D structures

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