The complete structure of an activated open sodium channel

Abstract

Voltage-gated sodium channels (Navs) play essential roles in excitable tissues, with their activation and opening resulting in the initial phase of the action potential. The cycling of Navs through open, closed and inactivated states, and their closely choreographed relationships with the activities of other ion channels lead to exquisite control of intracellular ion concentrations in both prokaryotes and eukaryotes. Here we present the 2.45 Å resolution crystal structure of the complete NavMs prokaryotic sodium channel in a fully open conformation. A canonical activated conformation of the voltage sensor S4 helix, an open selectivity filter leading to an open activation gate at the intracellular membrane surface and the intracellular C-terminal domain are visible in the structure. It includes a heretofore unseen interaction motif between W77 of S3, the S4–S5 interdomain linker, and the C-terminus, which is associated with regulation of opening and closing of the intracellular gate.

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

“…The deviations increase above 10 A at the C-terminal halves of the inner helices, which contain residues contributing to the activation gate; positions of these residues obviously differ between the open-and closed-state structures. Alpha carbon deviations of the open-state sodium channels NavAb 6 and NavMs 4 from the open-state Kv1.2 are rather small all along the S6 helices (Fig. 2B).…”

“…However, upon the 180 twist of the N i20 side-chain torsion x 2 , bonds C g -NH 2 and C g = O in the amide group would swap. The two orientations of the amide group would be hardly distinguishable in the 2.45 A resolution crystal structure, 4 but in the swapped conformations the Hbonds N Xi20 _NH-S_M (X-1)i30 would be formed. The NH-S hydrogen bonds are seen in X-ray structures of both small molecules and proteins.…”

“…22 Prokaryotic sodium channels NavAb and NavMs lack polar residues in positions i29. In the X-ray structure of the open-state NavMs, 4 asparagines N Xi20 apparently lack polar contacts and form tight intersegment contacts with sidechains of hydrophobic residues I (X-1)i26 , M (X-1)i30 and V Xo9 . This fact seemingly argues against the proposition that inter-subunit open-state H-bonds involving N i20 are common for sodium and calcium 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.…”