Movie frames were aligned to correct the drift and beam-induced motion with the program MotionCor2 (44), and the contrast transfer function of each aligned micrograph was estimated with the program Gctf (45). Particles from several representative micrographs were manually boxed using the e2boxer.py program from the EMAN 2.1 package (46), which were then used as reference for autopicking particles of whole data set with the program RELION 2.0 (47). All extracted particle images underwent multiple rounds of 2D classifications, and the classes that exhibited identifiable secondary structures features were rated as “good” ones. Particles in good classes were used to generate initial 3D models with the random model method in the program AUTO3DEM (48) and were further processed for 3D image reconstructions with the program RELION 2.0. The resolutions of maps were estimated using gold-standard criteria with the Fourier shell correlation (FSC) cutoff = 0.143 (49). Local resolution variations were estimated using the program ResMap (50).

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