Fig. 3: The DOM1h-574-208 nanobody disrupts the ordered binary cluster of the TNFα-TNFR1ecto complex. | Nature Communications

Fig. 3: The DOM1h-574-208 nanobody disrupts the ordered binary cluster of the TNFα-TNFR1ecto complex.

From: Highly ordered clustering of TNFα and BAFF ligand-receptor-intracellular adaptor complexes on a lipid membrane

Fig. 3

a Composite electron density map of the TNFα-TNFR1ecto-DOM1h nanobody complex in solution. TNFα, TNFR1ecto, and DOM1h are shown in blue, purple, and red, respectively. Focused refinement was performed on one of the three DOM1h nanobody regions in the map, after which maps for the remaining two nanobodies were generated by applying threefold symmetry. b Representative (n = 6408) image (left) and 2D class averages (middle) of the TNFα-TNFR1ecto-DOM1h nanobody complex in solution. The electron densities correspond to the bound nanobodies are highlighted with dashed red circles on the right panel. c Representative (n = 634) image (left) and 2D class averages (middle) of the TNFα-TNFR1ecto-DOM1h nanobody complex bound to the lipid monolayer. The proportion of protein particles belonging to each cluster is indicated in parentheses. The electron densities correspond to the bound nanobodies are highlighted with dashed red circles on the right panel. d Cryo-EM electron density map of the distorted binary cluster of the TNFα-TNFR1ecto-DOM1h nanobody complex bound to the Ni-NTA lipid layer. TNFα and TNFR1ecto are shown in blue and purple, respectively. e Superimposition of TNFR1ecto structures. TNFR1ecto in the ordered TNFα-TNFR1ecto binary cluster, the crystal structure, and the distorted TNFα-TNFR1ecto-DOM1h binary cluster are shown in purple, gray, and red, respectively.

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