Fig. 4: Structural and computational characterization of the TP-shell interaction. | Nature Communications

Fig. 4: Structural and computational characterization of the TP-shell interaction.

From: Structural basis for peroxidase encapsulation inside the encapsulin from the Gram-negative pathogen Klebsiella pneumoniae

Fig. 4

a Cutaway view of a KpEnc encapsulin model – obtained from a SUMO-TP_Enc sample – in surface representation (blue) highlighting bound SGSLNIGSLK TPs (orange). b Cryo-EM density highlighting the TP binding site (left). The KpEnc encapsulin interior surface (gray) along with density observed for the TP (orange) are shown. Corresponding structural model of the TP binding site (right). The KpEnc protomer (blue, ribbon) and TP (orange, stick) are shown. c Side view of the TP binding site with the interacting TP residues – SGSLNIGSLK – shown in mesh and ball and stick model representation. The shape complementarity and hydrophobic pocket of the encapsulin shell protein (hydrophobic surface representation) and the three hydrophobic TP residues L340, I342, and L345 (yellow boxes) are highlighted. d KpEnc protomer in surface representation colored by residue conservation as calculated via ConSurf analysis (left). The yellow outline indicates all residues within 5 Å of the bound TP (orange, stick representation). Magnified view of the TP binding site (right). Encapsulin shell protein residues within 5 Å of the TP are shown in ball and stick representation. Key hydrophobic and ionic interactions are highlighted. e ConSurf scores for the TP binding site residues of the encapsulin shell protein within 5 Å of the bound TP. Source data are provided as a Source Data file.

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