Crystal Structure of Der f 7, a Dust Mite Allergen from Dermatophagoides farinae

10.1371/journal.pone.0044850PLoS ONE79

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IgE epitopes of Der f 7.

<p>Ribbon diagrams of (A) Der f 7 and (B) Der p 7 showing locations of the putative IgE binding epitope residues of Der f 7, Leu48, Phe50 and Asp159, and their corresponding locations on Der p 7. These residues were plotted as both ball-and-stick and surface models with 50% transparency. Residues 48 and 50 are colored blue, while residue 159 is colored red. The diagrams were generated using the program Chimera <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044850#pone.0044850-Pettersen1" target="_blank">[37]</a>.</p

Ligand binding of Der f 7.

<p>¹H-¹⁵N HSQC spectra of 0.5 mM Der f 7 in the absence (black) or presence (red) of (A) juvenile hormone III (JH3); (B) methoprene; and (C) polymyxin B (PB) at a molar ratio of 1∶1 (protein:ligand). (D) Ribbon diagram of Der f 7 showing locations of residues that had their combined NH and ¹⁵N chemical shift values perturbed by more than 0.3 ppm in the presence of PB. These residues are presented in ball-and-stick models and colored red. The figure was generated using the program Chimera <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044850#pone.0044850-Pettersen1" target="_blank">[37]</a>.</p

Comparison of the structures of Der f 7 and Der p 7.

<p>(A) Superposition of the crystal structures of Der f 7 and Der p 7 prepared using the TopMatch web service <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044850#pone.0044850-Sippl1" target="_blank">[35]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044850#pone.0044850-Sippl2" target="_blank">[36]</a>. The root-mean-square-error of superposition of Der f 7 and Der p 7 is 0.97 Å for 186 structurally equivalent Cα atoms. Der f 7 is colored cyan and Der p 7 is colored red. Pairs of structurally equivalent residues are colored yellow (Der f 7) and blue (Der p 7). The figure was generated using PyMol <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044850#pone.0044850-DeLano1" target="_blank">[33]</a>. (B) Non-conserved residues between Der f 7 (blue) and Der p 7 (red) are shown as ball-and-stick models on the superimposed structures of Der f 7 and Der p 7. Non-conserved residues that are also surface exposed are colored cyan (Der f 7) and yellow (Der p 7), including Asp18/Glu18, Gln25/Lys25, Ala38/Ser38, Val45/Ile45, Leu48/Ile48, Phe50/Leu50, Ala55/Asp55, Glu60/Gln60, Gln70/Val70, Gly77/Ser77, Glu79/Asp79, Ile81/Val81, Ile94/Val94, Thr111/Asn111, Ala124/Glu124, Asp131/Glu131, Lys179/Ala179, Arg191/Lys191 and Lys195/Arg195, respectively. The figure was generated using Chimera <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044850#pone.0044850-Pettersen1" target="_blank">[37]</a>.</p

Crystallographic data statistics of the structure of Der f 7.

<p>Rsym  =  Σ |<i>Ii – <i></i>|/Σ |<i>Ii</i>|, where <i>Ii</i> is the intensity of the <i>i</i>th measurement and <i><i></i> is the mean intensity for that reflection.</i></i></p><p><i><i>Rcryst  =  Σ ||Fo| – |Fc||/Σ |Fo| calculated from the working data set.</i></i></p><p><i><i>Rfree was calculated from 5% of data randomly chosen not to be included in refinement.</i></i></p><p><i><i>Ramachandran results were determined by using PROCHECK.</i></i></p

Crystal structure of Der f 7.

<p>(A) Topology diagram of Der f 7. The 4-stranded β-sheet is colored yellow and the 5-stranded β-sheet is colored green. (B) Ribbon diagram of Der f 7 is colored based on the B-factor spectrum, with a range from 13.59 (blue) to 70.52 (red). The loop region between β1 and β2 is labeled as the “epitope region”. The figure was generated using the program PyMol <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044850#pone.0044850-DeLano1" target="_blank">[33]</a>. (C) Two different views of the surface charge diagram of Der f 7. The positively and negatively charged residues are colored blue and red, respectively. The diagram was generated using the program Molmol <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044850#pone.0044850-Koradi1" target="_blank">[34]</a>.</p