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. Author manuscript; available in PMC: 2016 Jan 16.
Published in final edited form as: J Mol Biol. 2014 Aug 23;427(1):3–30. doi: 10.1016/j.jmb.2014.08.010

Figure 5. BacNaV PD sequence conservation.

Figure 5

(a) Conservation analysis of the BacNaV PD, measured by the relative statistical entropy at each position, 115, mapped on the NaVAe1p sequence. Highly conserved positions in rank order starting with the most conserved are colored dark blue, light blue, and green. Other positions of interest are colored yellow. (b) Conservation analysis depicted on two subunits of NaVAe1p. Select positions of interest are shown as sticks and are labeled. (c) Spacefilling model of panel (b). (d) Extracellular view of a single PD subunit. Black circle marks the location of the ion conductive pore of the SF. (e) The highly conserved S6 Trp sidechain (Trp195 in NaVAb, shown in green spheres; Trp215 in NaVAe1p) is adjacent to a membrane phospholipid that appears to be well ordered as a lipid or detergent molecule in most available BacNaV structures. Different channel subunits are colored white, yellow, and slate. The fourth subunit is not visible. Red mesh is from an FO-FC omit map calculated at 2.7 Å from PDB 3RVY with the “pore lipid” omitted from the calculation, contoured at 2.5σ. This density likely represents a phosphatidylcholine molecule that is present at high concentrations in the NaVAb crystallization condition. (f) Sequence alignment of S6 segments from BacNaVs, CaV, and NaVs. Colors match those in panels ‘(a)-(d)’. Sequences identities are; NaVBh1 (NaChBac)(NP_343367.1), 207-240; NaVAb (YP_001490668.1), 211-244: NaVRh (PDB:4DXW), 195-228; NaVAe1 (YP_741167.1), 213-246; NaVCt (WP_007502948.1), 210-243; NaVMs (YP_864725.1), 115-129; NaVSp1 (YP_165303.1), 192-225; CaV1.2 (CAA84346), IS6 380-413, IIS6 728-761, IIIS6 1141-1174, IVS6 1451-1484; CaV2.1 (NG_011569.1), IS6 335-368, IIS6 689-722, IIIS6 1488-1521, IVS6 1786-1819; CaV3.1 (O43497), IS6 370-403, IIS6 939-972, IIIS6 1512-1545, IVS6 1826-1860; NaV1.4 (NP000325.4), IS6 422-455, IIS6 777-810, IIIS6 1270-1303, IVS6 1573-1606; NaV1.7 (NM_002977), IS6 377-410, IIS6 932-975, IIIS6 1421-1454, IVS6 1724-1757.