Figure 3
Stable conformation of the Nsp15 monomer. (a) Free energy landscape obtained by MSM. The inset shows a close-up view around the global free energy minimum (GM). I1, I2, and I3 represent three intermediates, and apoH indicates the crystal conformation. (b) Visualization of GM (red) superimposed onto one monomer of apoH (blue) in the hexameric state by best-fitting Mid and C-term domains. (c) Comparison of the GM (red), I1 (cyan), I2 (orange), and I3 (blue) conformations superimposed onto the Mid and C-term domains. (d) Result of DynDom3D analysis between GM and apoH, shown by the apoH conformation. The red arrow indicates the rotational axis of the dynamic domain (cyan) rotation, which corresponds to N-term domain. (e) Inter-domain salt bridges in the GM, apoH, and UTPH conformations. The apoH conformation is shown in white. N-term (blue), Mid (red), and C-term (dark grey) domains of the GM conformation and UTPH conformation (pink) are superimposed on the apoH conformation (white) by best-fitting Mid domain. The green lines connecting ARG199 and LYS205/ASP297 indicate the salt bridges maintained in all the conformations. The magenta lines between LYS71 and ASP273 represent the salt bridge formed in apoH and UTPH, and the orange line between LYS71 and ASP92 shows the salt bridge established solely in GM. (d) was created using Rasmol61.
