Structures of 4E10, b12, 2F5, the CL-binding yeast cytochrome bc1 complex and Annexin V.

<p>(<b>A</b>) The structure of the Fv domain of 4E10 (from 2FX7.pdb <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003639#ppat.1003639-Cardoso1" target="_blank">[9]</a>) is shown in a semi-transparent molecular surface representation colored by electrostatic potential (blue: positive; red: negative). Side-chains of key residues are shown in licorice-stick representations and labeled. In this orientation, the V_L domain is in the upper left and the V_H domain is in the lower right. The backbone of the epitope peptide co-crystallized in this structure is shown in a cartoon representation, with side-chains shown in licorice-stick representations colored by atom-type (carbon: gray; oxygen: red; nitrogen: blue). (<b>B</b>) The molecular surfaces of the Fv domains of 4E10 (top) and 2F5 (bottom) are shown, oriented with V_L domains at left and the V_H domains at right. The surface is colored to show hydrophobic patches, defined by the program HotPatch <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003639#ppat.1003639-Pettit1" target="_blank">[113]</a>; patches are colored in descending order of total area (red, orange, yellow …). Key residues and hydrophobic patch areas are indicated. (<b>C</b>) The structure of the Fv domain of b12 (from 3RU8.pdb <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003639#ppat.1003639-Azoitei1" target="_blank">[104]</a>) is shown as in (<b>A</b>). (<b>D</b>) Annexin V (1A8A.pdb <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003639#ppat.1003639-Swairjo1" target="_blank">[114]</a>) is shown as a semi-transparent molecular surface colored by underlying atom type, highlighting the exposed tryptophan side-chain (shown in licorice-stick representation). Calcium ions, shown as green spheres, coordinate the phosphate moiety from PS (shown in a licorice-stick representation, colored by atom-type as in (<b>A</b>) plus phosphorus in orange). (<b>E</b>) The structure of the unbound form of 4E10 (4LLV.pdb) is shown as a semi-transparent molecular surface representation colored as in (<b>A</b>). Side-chains of key residues are shown in licorice-stick representations and labeled. The view of the molecule has been rotated roughly 45° from the orientation of 4E10 shown in (<b>A</b>). The coordinated SO₄ ion is shown in a licorice-stick representation colored by atom type as in (<b>A</b>) plus sulfur in yellow. (<b>F</b>) CL is shown docked onto the unbound structure of 4E10 oriented and colored as in (<b>E</b>). Molecular images were generated with MacPyMOL <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003639#ppat.1003639-DeLano1" target="_blank">[109]</a>.