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. 2016 Dec 6;6:38101. doi: 10.1038/srep38101

Figure 1. Secondary and tertiary structural prediction of H. pylori CagL (strain 26695); the selection of ten short motifs for generating deletion mutants is indicated with regard to the recently solved CagL crystal structure.

Figure 1

(A) Placement of the ten motif deletion mutants within the secondary structure of CagL. Secondary structure prediction was performed using Jpred (www.compbio.dundee.ac.uk/jpred). Alpha helices are indicated by red symbols, beta sheets are indicated by blue symbols. Only the structured regions of confidence score ≥1 of the Jpred prediction are indicated by symbols below the sequence. SP designates a predicted leader peptide which probably serves to transport CagL to the periplasm. (B) Placement of the ten motif deletion mutants in the CagL crystal structure (pdb: 3zcj_chainA38), which was imaged in ribbon mode by Yasara (www.yasara.org). Motif deletion mutants along the 2D and 3D structure are indicated in blue (2D) and in different colors (3D structure; pink, turqoise, red, purple, yellow) contrasting to the backbone shown in royal blue. The probably disordered regions (“loops”) within CagL which correspond to predicted loop regions in a CagL structural prediction (not shown) are indicated and numbered as loop 1 through loop 4 in B (also indicated as loops with the same numbering in Supplementary Fig. S2). The TSPSA motif was not structurally resolved in the crystal (3D) structure pdb: 3zcj_chainA and therefore is not indicated in B (loop 1).