Fig. 3: Characterization of the nCoV400Fab-N-CTD interface. | Communications Biology

Fig. 3: Characterization of the nCoV400Fab-N-CTD interface.

From: Structural basis of a human antibody targeting SARS-CoV-2 nucleocapsid protein dimerization domain and interfering with RNA-binding

Fig. 3

a The overlook of three main epitopes of N-CTD recognized by nCoV400Fab in the crystal structure. The nCoV400Fab is shown in a ribbon representation while the N-CTD dimer is shown in an electrostatic surface representation. b, c The first epitope (250–257) of N-CTD (cornflower blue) is recognized by nCoV400Fab VL1-CDR1,3 (medium purple) and VH1-CDR2-3 (dark magenta) via numerous hydrogen bond interactions and π-stacking interactions in the left panel. The interacting residues of N-CTD and nCoV400Fab are highlighted with the stick representation (left panel). The hydrogen bonds are shown as dashed lines. The VL1-CDR1,3 and VH1-CDR2-3 of nCoV400Fab are shown in an electrostatic surface representation in which blue denotes a positive charge potential while red indicates a negative charge potential (right panel). d Recognition of K257 in N-CTD by VL1-CDR1-2 of nCoV400Fab with the stick representation (left panel), and the interacting residues of nCoV400Fab are illustrated in an electrostatic surface representation (right panel). e The second epitope of N-CTD is recognized by nCoV400Fab VL2-CDR2 (light pink) via hydrogen bond interactions and hydrophilic interactions. f The third epitope of N-CTD recognized by nCoV400Fab VH2-CDR3 via hydrogen bonds interactions and π-stacking interactions.

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