Figure 2: Inner and outer cores of YdaH.
From: Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual topology
(a) The inner core of YdaH, comprising TMs 1, 2, 5, 6 and 7 (coloured slate), contributes to dimerization as well as formation of a frame-like structure housing the outer core of the protomer. The outer core of YdaH is composed of TMs 3, 4, 8, 9 as well as HPs 1 and 2 (coloured yellow). (b) The outer core of YdaH forms a channel (coloured purple) spanning approximately from the middle of the inner membrane up to the periplasmic space. This channel was calculated using the programme CAVER ( http://loschmidt.chemi.muni.cz/caver). The secondary structural elements of the YdaH protomer are in yellow. Residues D180, N390, W400, P418, R426, D429 and N433 are in green sticks. The bound sodium ion is shown as an orange sphere. (c) The bound Na+ (orange sphere) is found to coordinate with N390, G394, D429, N433 and a water molecule (red sphere). The Fo–Fc map, showing the bound Na+ and H2O, is contoured at 3.0 σ (blue mesh).
