Fig. 3: AL59 adopts a fold related to λ3-FOR005, but harbours an extended constant domain (CL) fragment in its amyloid core.
a Sequence alignment of AL59 belonging to the λ3 gene to the four other ex vivo LC amyloid structures λ3-FOR005 [https://www.rcsb.org/structure/6Z1O], λ6-AL55 [https://www.rcsb.org/structure/6HUD], λ1-FOR001 [https://www.rcsb.org/structure/7NSL] and λ1-FOR006 [https://www.rcsb.org/structure/6IC3]. β-strands and strict β-turns are indicated by numbered β and non-numbered TT symbols, respectively. Strict sequence identity is indicated by a red box with white character, similarities within and across groups are indicated by red characters and blue frames, respectively. Secondary structure elements of λ3-AL59 and λ3-FOR005 are shown above. CDR segments of λ3-AL59 and λ3-FOR005 are labelled and highlighted in yellow and orange, respectively. The CL-derived fragment in the amyloid core of AL59 is highlighted in light pink. b The AI-generated native AL59 structure (left) is compared to the amyloid structure (right). VL and CL domains are coloured white and light pink, respectively. The CDRs are coloured yellow and labelled. The non-amyloidogenic CL part is semi-transparent. Modified N- and C-termini of LC peptide fragments detected by LC-MS/MS are shown as red and blue Cα-spheres, respectively. The residue-level line-plot depicts the domain boundaries and modified N- and C-termini of LC fragments detected by LC-MS/MS. c The superimposed λ3-AL59 and λ3-FOR005 structures are shown as white and black cartoons, respectively.
