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. 2022 Apr 5;13:1825. doi: 10.1038/s41467-022-29416-z

Fig. 4. Structural and bioinformatic analysis of closed state-stabilizing mutations.

Fig. 4

a Zoomed-in views of space A- and D-stabilizing mutations in the N1-CA09-sNAp-155 cryo-EM structure and corresponding regions in predominantly open N1 (PDB ID 4B7Q) and predominantly closed N2 (PDB ID 6BR5) and N5 (PDB ID 3TI8) NAs. The red spheres highlight the positions of cavities in space A or space D. b Descriptions of color labels which apply to panels a and d. c Sequence logos of a highly conserved residue (the main catalytic residue), a representative position with an entropy near the mean for the whole protein, and the position of maximum entropy within both the N1 and N2 subtypes are shown for comparison with panel d. d Sequence logos for N1-CA09-sNAp-155 and naturally occurring NAs at positions that can alter NA tetrameric conformation. All data for panels a and d is derived from a compiled database of all unique sequences from each subtype prior to December 31st, 2019. e (Top) Spaces A and D in a representative crystal structure of an N8 NA (PDB ID 4WA5) and (bottom) design model for space D of N8-JD13-sNAp-285. The red sphere highlights the position of a cavity in space D. f Mutation schematics and NS-EM comparing N8-JD13-WT, N8-JD13-sNAp-282, and N8-JD13-sNAp-285 (scale bar, 10 nm). NS-EM was performed and analyzed multiple times and representative images are shown.