Figure 4: Structural comparison of IP39 protomers.

(a) EM density map containing approximately two unit cells is shown by mesh representation at 1.4σ, viewed from the luminal side. Unique molecular densities in strand B are coloured magenta (Mol1), cyan (Mol2) and yellow (Mol3). The molecules shown with the same colours are related by crystallographic symmetry. The black bar represents 20 Å. (b,c) Only the EM density of the three coloured molecules in a are shown by removing the other densities for clarity and viewed nearly parallel to the membrane plane (b). The three isolated molecules are superimposed (c) and the two sides of the densities are indicated as ’Nock‘ and ’Point‘. The black bars represent 10 Å. (d,e) Ribbon models of a four-helical bundle protein (PDB: 2UUI) are fitted to the EM density map (light grey mesh contoured at 1.3σ, putative transmembrane region only) of the three molecules in strand B. The fitted model helices are represented by magenta, cyan and yellow ribbons superimposed on Mol1, 2 and 3, respectively, viewed perpendicular (d, from the same direction with a) and parallel (e, the upper side is the ’Nock‘ side) to the membrane plane. The white bars represent 10 Å. (f) A schematic diagram representing the arrangement, directions and spacing of the IP39 protomers in a single strand viewed perpendicular to the membrane plane by the black and white circles. The black semicircular side indicates the large protruding side in the cytosolic region of the IP39 proteins.