Extended Data Figure 1 . Cryo-EM, single-particle analysis of human γ-secretase.

a, Representative raw particles from an original micrograph. b, Representative reference-free 2-D class averages of the γ-secretase particles. Two classes identified by a red rectangle box (lower right corner) may contain some density for the extended cytosolic loop sequences between TM6 and TM7 of PS1, which are disordered in the final maps. c, Resolution estimation of the EM structure. The overall resolution is calculated to be 3.4 Å on the basis of gold-standard FSC curve⁴². d, Color-coded resolution variations in the γ-secretase structure as estimated by ResMap⁴⁴. e, FSC curves of the final, Refmac-refined model versus the map it was refined against (in black); of a model refined in the first of the two independent maps used for the gold-standard FSC versus that same map (in red); and of a model refined in the first of the two independent maps versus the second independent map (in green). The small difference between the red and green curves indicates that the refinement of the atomic coordinates did not suffer from severe overfitting.