Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel

Abstract

Voltage-gated sodium (Nav) channels are essential for the rapid depolarization of nerve and muscle1, and are important drug targets2. A family of bacterial Nav channels, exemplified by NaChBac (Na+-selective Channel of Bacteria)3, provides a good model system for structure-function analysis. Here we report the crystal structure of NavAP, a NaChBac orthologue from marine bacteria alpha proteobacterium HIMB114, at 3.05 Å resolution. The channel comprises an asymmetric tetramer. The carbonyl oxygen atoms of Thr178 and Leu179 constitute an inner site within the selectivity filter (178TLSSWE183) where a Ca2+ can bind and resides in the crystal structure. The outer mouth of the Na+ selectivity filter, defined by Ser181 and Glu183, is closed, as is the activation gate at the intracellular side of the pore. The voltage sensors adopt a depolarized conformation with all the gating charges exposing to the extracellular side. We hypothesize that NavAP is captured in an inactivated conformation. Comparison of NavAP with NavAb4 reveals significant conformational rearrangements that may underlie the electromechanical coupling mechanism of voltage-gated channels.

Molecular basis of ion permeability in a voltage‐gated sodium channel

“…The structures of several prokaryotic sodium channels in different functional states (Payandeh et al , 2011, 2012; McCusker et al , 2012; Zhang et al , 2012; Bagnéris et al , 2013, 2014, 2015; Tsai et al , 2013; Shaya et al , 2014) have been solved by X‐ray crystallography or electron microscopy. Functional studies on wild‐type and mutant prokaryotic channels (Ren et al , 2001; Yue et al , 2002; McCusker et al , 2011; Shaya et al , 2011; Tang et al , 2014) have suggested which regions and residues may be important for ion binding, selectivity and translocation within the SF.…”

Conservation and variability of the pore-lining helices in P-loop channels

“…When the first X-ray structures of potassium channels become available, 2,11 various sequence alignments were proposed between these channels and medically important sodium and calcium channels. 3,[12][13][14] More recent 3D structures of sodium, 4,6,7,10 calcium, 9 TRPV1 15 and two-pore 16 channels opened a possibility to obtain 3D alignment of various P-loop channels, compare sequence-based and 3D-based alignments and analyze similarity and differences of these channels. Results of this comparison reveal some problems in sequence alignments that previously seemed unambiguous.…”

“…[1][2][3][4][5][6][7] and cryoelectron microscopy, e.g. 8,9 Voltagegated channels (4 £ 6TM) have four voltage-sensing domains and a pore domain.…”

Asymmetric perturbations of signalling oligomers

“…A comparison of the XRC structures of bacterial NavRh and NavAb showed structural asymmetry for the activated voltage-sensing domains (S1-S4) and the EC entrance of the selectivity filter (Payandeh et al, 2011;Zhang et al, 2012). Based on XRC snapshots of two inactivated states of NavAb, the S6 segments seem to collapse asymmetrically into a dimer-of-dimers conformation at the activation gate .…”