Extended Data Fig. 3: Cryo-EM density maps and model docking of human Vγ9Vδ2 or Vγ5Vδ1 TCR–CD3 complex.

a, The representative cryo-EM densities for TMs of the Vγ9Vδ2 TCR–CD3 complex shown as transparent surface and contoured at 3σ. b, The cryo-EM densities for segments in one ECD of Vγ5Vδ1 TCR–CD3 complex shown as transparent surface and contoured at 3σ. c, Local cryo-EM density of representative interchain interface between Vγ5_I and Vγ5_II shown as transparent surface and contoured at 3σ. The model for Vγ5_I and Vγ5_II are coloured in hot pink and grey, respectively. d, Docking of the atomic model of Vγ9Vδ2 TCR–CD3 complex into the MPD_I/TMD_I and the MPD_II/TMD_II maps, respectively. Insets: the cholesterol molecule fits well with the corresponding density. e, Docking of MPD/TMD map into the overall map. The inset shows a good match between the features of MPD_I and MPD_II in the MPD/TMD map and those in the overall map. f-g, Docking of MPD_I/TMD_I and MPD_II/TMD_II maps into the MPD/TMD EM map, respectively. The inset shows a good match between the features in the TMD_I and TMD_II maps and those in the MPD/TMD map. h, Docking of ECD map into the overall map. The inset shows a good match between the features of the ECD map and those in the overall map. i, Docking of ECD, MPD_I/TMD_I and MPD_II/TMD_II maps into the overall map. The overall, MPD/TMD, MPD_I/TMD_I, MPD_II/TMD_II, and ECD maps are contoured at 1σ, 2σ, 8σ, 8σ, and 9σ, respectively. The details of the docking strategy are described in the method section.