Extended Data Fig. 1: Sequence analysis of Bab/Agp and structural characterization of BASS11Bab.
From: Characterization of an amyloid-based antiphage defence system in Escherichia coli
a, An alignment of the sequence of the N-terminal region of selected bacterial Bab and Bell domain proteins, fungal Hell domain proteins and Avast2, bNACHT02, 11 and 23 NLRs involved in antiphage defence is given together with the domain and gene architecture in which the sequences occur. The color code is as in Fig. 1a, with amyloid forming sequences in blue and predicted N-terminal hydrophobic helix in red. Genbank entries for all mentioned gene products are given in Supplementary Table 1. b, Domain associations of BASS11-motifs. An alignment of BASS11-motifs occurring in different domain architectures is given. Corresponding domain architectures and the motif position (in blue) are given for each protein. Sequences grouped with a bracket accolade are encoded by adjacent genes. c, AlphaFold3 model of Agp. The TPR, GreA/B-C and PIN domains are given in cyan, blue and gold respectively. d, Structural characterization of Bab (50-109) fibrils by solid-state NMR spectroscopy. Top panel, excerpts of 2D 13C-13C correlation experiments recorded at 800 MHz 1H frequency, using mixing times of 50 ms (in black) and 150 ms (in red). Sequential assignment of the I87-G88-S89-V90 stretch is highlighted. Middle panel, excerpt of the aromatic region of the 2D 1H-13C INEPT, detecting disordered residues. Bottom panel, secondary chemical shifts for the stretch T85-V90. Positive or negative values correspond to α-helical or β-strand conformation, respectively. e, AlphaFold3 model of Bab(82-109) in multimeric form (with a sequence input of 6 monomers, ipTM=0.82, pTM=0.84), the positions of predicted β-strands are given in blue in the amino acid sequence. A consensus sequence logo of the BASS11 motif based on the alignment of Extended Data Fig. 1b is given. Position of conserved residues underlined in the sequence are given on the structural model, glycine residues interrupting the β-strands are given in grey and marked by asterisks. The boxed region corresponds to residues with spectral assignment in ssNMR for which chemical shift and thus secondary structure have been determined (Extended Data Fig. 1d). The model is consistent with chemical shifts experimentally determined by ssNMR. AF3 predictions for the BASS11Agp region were also performed but were of very low confidence.
