Extended Data Fig. 2: Cryo-EM dataset processing results and resolution of EcZorAB. | Nature

Extended Data Fig. 2: Cryo-EM dataset processing results and resolution of EcZorAB.

From: Structure and mechanism of the Zorya anti-phage defence system

Extended Data Fig. 2

a, A representative SDS gel of the purified EcZorAB complex. b, An EM image of the EcZorAB sample under cryogenic condition. c, Cryo-EM density map of EcZorAB coloured by local resolution (in Å) estimated in cryoSPARC. d, Gold standard (0.143) Fourier Shell Correlation (GSFSC) curves of refined EcZorAB complex. e, Cryo-EM map of EcZorAB. f, Representative model segment of ZorA fit into EM density, focusing on TM1 of one of the ZorA subunits. g, Volcano plot analysis, visualizing ratio and significance of change between all proteins quantified by mass spectrometry in E. coli total lysates either transformed with pEcZorI plasmids or not (Supplementary Table 1). Significance was tested via two-tailed two-sample Student’s t-testing with permutation-based FDR control, ensuring a corrected p-value of <0.01. n = 4 technical replicates derived from n = 3 culture replicates. h, Absolute copy number analysis of Zorya proteins expressed in E. coli. Determined via comparison of molecular weight-adjusted label-free quantified protein abundance values from this study, to known copy numbers reported by Schmidt et al. 57 and establishing a “proteomic ruler” for conversion of measured abundance values to approximate copy numbers (Supplementary Table 1). n = 4 technical replicates derived from n = 3 culture replicates. i, Soft mask used for local refinement of the ZorB PGBDs. j, Local refinement map of the ZorB PGBDs (made with the soft mask shown in i), coloured by local resolution. k, A representative of a model segment of the ZorB PGBDs fitted into of the local refinement EM density map shown in j, focusing on the PGBD dimerized interface. l, Fit of lipids found in the TMD of ZorA in the EcZorAB cryo-EM map. Images in a and b are representatives of at least 3 replicates.

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