Table 1.

Potential inter-transmembrane interactions in the VSD of the Ciona VSP

Residue3 Å4 Å5 Å
D129/S195 (S1)R2226 (S4)L157 (S2)A154 (S2)
R3318 (S4)C248 (S2)F161 (S2)
F252 (S2)E245 (S2)
D136/E202 (S1)K142 (S1–S2)Y150 (S2)D151 (S2)
Q147 (S2)G230 (S1–S2)I229 (S1–S2)
R2315 (S4)Y231 (S1–S2)
F241 (S2)
R1312 (S4)
A154/E245 (S2)R3318 (S4)L132 (S1)D129 (S1)
Y231 (S1–S2)T197 (S3)
Y285 (S3)R2226 (S4)
R2315 (S4)S195 (S1)
S198 (S1)
D164/E255 (S2)S188 (S1)I113 (S0)
F172 (N-terminal)
K4321 (S4)D278 (S3)
R168/R259 (S2)I113 (S0)E183 (S3)
F177 (S2–S3)G187 (S3)
D186 (S3)I190 (S3)
W169 (N-terminal)R3229 (S4)
F172 (N-terminal)R4232 (S4)
R5324 (S4)F269 (S3)
N275 (S3)
D278 (S3)
E183/N275 (S3)R4232 (S4)R5324 (S4)R168 (S2)
F256 (S2)
R259 (S2)
D186/D278 (S3)R5324 (S4)R168 (S2)F252 (S2)
R3229 (S4)E225 (S2)
R4232 (S4)F256 (S2)
K4321 (S4)R259 (S2)
T193/Y285 (S3)T246 (S2)L225 (S4)S158 (S2)
R2226 (S4)A222 (S4)
Y231 (S1–S2)Q233 (S1–S2)
F242 (S1–S2)
E245 (S2)
I249 (S2)
  • The conserved polar and charged residues in the S1–S3 transmembrane segments identified in Figure 1 were mapped onto the crystal structures of the Ciona VSD upstate crystal structure (bold, 4G7V; Li et al., 2014) and the Kv1.2/2.1 chimera crystal structure (black, 2R9R; Long et al., 2007). Amino acids within 5 Å are listed. The bold numbers correspond to the Ciona VSP sequence. The black numbers correspond to the Kv1.2/2.1 chimera crystal structure. The secondary structure of the residue is in parentheses. For example, (S1–S2) indicates the extracellular loop between S1 and S2. The putative position of the charged residue in S4 (R−1-X-X-R0-X-X-R1-X-X-R2-X-X-R3-X-X-R4-X-X-R5) is depicted as in Figure 1.