Fig. 8: Clustered structures of the BAFF-BAFFRfl-TRAF3 complexes.

a A hexa-histidine tag was attached to the N-terminus of BAFF, allowing the hisBAFF-BAFFRfl-TRAF3 complex to bind to the Ni-NTA lipid monolayer. The head groups of Ni-NTA lipids are indicated in green. “H” denotes the histidine tag. Created in BioRender. Lim, C. (2025) https://BioRender.com/z6b5t4x. b Bottom view and c side view of the cryo-EM map of the hisBAFF-BAFFRfl-TRAF3 cluster. The BAFFR intracellular domain and TRAF3 proteins are colored orange and blue, respectively. Alpha helical rods from the second TRAF3 cluster are shown in gray. Focused refinement of the TRAF3 cluster region was performed for 3D map reconstruction. d Side view of the cryo-EM map of the hisBAFF-BAFFRfl-TRAF3 cluster without the focused refinement of the TRAF3 region. The structures of BAFF, BAFFR, and TRAF3 are fitted into the map. The map, BAFF, BAFFR, and TRAF3 proteins are shown in gray, green, orange, and blue, respectively. Due to structural flexibility, only part of the TRAF3 coiled-coil helices are visible. The missing segments of the TRAF3 coiled-coil helices were predicted using AlphaFold3. e Top view of the cryo-EM map of the hisBAFF- BAFFRfl-TRAF3 cluster without focused refinement. The map corresponding to the extracellular side of the hisBAFF-BAFFR-TRAF3 cluster is shown in light cyan. The structures of three BAFF-BAFFRecto trimers are fitted into the map. f An octa-histidine tag was attached to the N-terminus of TRAF3, allowing the BAFF-BAFFRfl-hisTRAF3 complex to bind to the Ni-NTA lipid monolayer. The head groups of Ni-NTA lipids are indicated in green. “H” denotes the histidine tag. Created in BioRender. Lim, C. (2025) https://BioRender.com/z6b5t4x. g Top view and h side view of the electron density map of the BAFF-BAFFRfl-hisTRAF3 cluster. The BAFFR intracellular domain and TRAF3 are colored orange and blue, respectively.