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. Author manuscript; available in PMC: 2019 Apr 3.
Published in final edited form as: Structure. 2018 Mar 15;26(4):619–626.e3. doi: 10.1016/j.str.2018.02.014

Figure 4. Model and density comparison among models and densities via longitudinal section.

Figure 4

(A) Conformation 1 model (purple), conformation 1 density (pink, displayed at 3 σ) and docked segmented Gag dimer (PDB 1AFV, red). (B) Conformation 2 model (olive), conformation 2 density (yellow, displayed at 3.7 σ) and docked Gag dimer (red). (C, D) utilizing similar color code with (A) and (B), respectively, with higher visualization threshold (displayed 6.2 σ and 5.1 σ for conformation 1 and 2, respectively). PDB 4V60 (grey) is docked into conformation 1 and conformation 2 density. C-terminus of Gag and N-terminus of MVP is connected by flexible linker, shown as dashed line. (E) Local resolution estimation of conformation 2 density map calculated by Resmap (Kucukelbir et al., 2014). The flexible region is of low resolution and appear blue (fused protein at waist, C terminus near cap and inner surface). The major conformational change takes place at shoulder domain but the resolution is relatively high.