Extended Data Fig. 2: Cryo-EM analysis of the human Vγ9Vδ2 TCR–CD3 complex in LMNG or GDN detergent micelles.

a-b, Representative cryo-EM micrographs (a) and 2D class averages (b) of the Vγ9Vδ2 TCR–CD3 complexes in the LMNG detergent micelles. Scale bar: 50 nm. c-g, 3D reconstruction analysis of Vγ9Vδ2 TCR–CD3 complex in the LMNG detergent micelles. The final 3D reconstruction evaluated by the 0.143 FSC criterion (blue line) (c). Local-resolution estimation of final 3D reconstruction sharpened by DeepEMhancer⁶⁴. The map is contoured at 3σ (d). Angular distribution of the Vγ9Vδ2 TCR–CD3 complex particles in the final round of 3D refinement using CryoSPARC⁵⁹ (e). FSC curves were generated to compare the refined models with the overall maps for refinement (black), as well as between each model refined in one of the two independent maps used for the FSC and the same map (red), and between the same model and the second independent map (green) (f). The 3DFSC sphericity plot generated using 3DFSC⁶⁶ (g). h-j, 3D reconstruction analysis of Vγ9Vδ2 TCR–CD3 complex in the GDN detergent micelles. The final 3D reconstruction evaluated by the 0.143 FSC criterion (h). Local-resolution estimation of final 3D reconstruction. The map is contoured at 4σ (i). The 3DFSC sphericity plot. This plot was generated using 3DFSC⁶⁶ (j). k, The conformations of Vγ9Vδ2 TCR–CD3 complex resolved in LMNG and GDN detergent micelles are almost the same, with a RMSD of 1.3 Å over 107 aligned Cα atom pairs.