Fig. 6: TCR–CD3 resting state conformational variability.
From: The resting and ligand-bound states of the membrane-embedded human T-cell receptor–CD3 complex
a Comparison of ND-I (transparent cyan) and ND-II (red) model surfaces, aligned on the TCRα TM helix. b, c Cartoon representation of select domains in ND-I (cyan) and ND-II (red), highlighting domain movements between them (gradient arrows). d TCRβ and CD3γ TM helices move away from the ND-I cholesterol-binding site in the transition to ND-II. Arrows indicate accompanying cholesterol movements. e Comparison of the TCRα and CD3δ lateral glycosylation sites (red and cyan dashed lines, respectively) in the maps, with stacking of the glycan array on ectodomain closure (purple dashed line). Insets highlight N-linked glycan cores modeled into these densities in GDN and ND-I. f Comparison of the CD3δ N38 residue in GDN, ND-II and ND-I. Gray surface is the locally refined, DeepEMhancer-sharpened map. g Modeling HLA (gray) binding to the TCR–CD3 by docking the TCR–HLA crystal structure 2BNQ59. Cross section through the modeled HLA–TCR interface in ND-I with the ND-I model surfaces (h) or locally refined, DeepEMhancer-sharpened map (i) shown.
