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. 2022 Sep 20;3:e16. doi: 10.1017/qrd.2022.13

Fig. 1.

Fig. 1.

Models obtained from AlphaFold2 and the refinements using Cryo-EM map 23274–7LCI-R (EMDB-PDB-chain ID) and hybrid density maps at 6 and 8 Å resolutions. (a) Superposition of the protein structure (red, chain R of 7LCI) and the model obtained from AlphaFold2. (b1) The box-cropped region of cryo-EM map 23274 (EMDB ID, cyan) superimposed with the model (blue) refined using Phenix and the cryo-EM map. (b2) Superposition of the structure (red, chain R of 7LCI) and the refined model (blue) using Phenix and the box-cropped cryo-EM map in b1. Hybrid density maps of 6 Å (grey in c1) and 8 Å (yellow in d1) resolutions are superimposed with the corresponding models refined from the maps, respectively. The 6 Å-map-refined model (Cyan ribbon in c1, c2) and 8 Å-map-refined model (green in d1, d2) are superimposed with the structure (red) in c2 and d2. The superposition of two atomic models was performed with TM-align (Zhang and Skolnick, 2005) in all figures. The superposition of a density map and a model was performed using Phenix (Terwilliger et al., 2022) in all figures. An example of a weaker density region in the cryo-EM map and in the corresponding hybrid maps is indicated by an ellipse in b1, c1, and d1.