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![[Figure 2]](ic5119fig2mag.jpg)
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Figure 2
Global motions from structural comparisons illustrated for the GluA3 glutamate receptor N-terminal domain dimer. (a, b) Comparison of two structures by calculating a deformation vector between corresponding atom positions (a) and a morph (b). A view from one perspective shows an inter-subunit counter-rotation, resulting in a transition from displaced to parallel lower lobes. (c, d) Ensemble analysis using multiple structures (c) and PCA (d). A projection onto the subspace of the first two PCs (d) (left) allows a mapping of the conformational space of the structural ensemble in (c) (blue points labelled with PDB and chain IDs corresponding to the respective dimers) as well as the conformations from the morph in (b) (red points); the values along the axes show the r.m.s.d. contributed by PC1 and PC2 from the average at the origin. PC1 (x axis of the projection) accounts for most of the variation between the red points, supporting its correspondence to the displaced → parallel transition in (b), in line with PC1 having a directional overlap (correlation cosine) of 0.98 to the deformation vector. By contrast, PC2 (y axis) features an opening and closing motion of the lower lobes. This motion can be visualized by adding PC2 to the average conformer (in this case with 1/8 of its variance) in the positive and negative directions, generating two new structures, which are marked by grey points on the plot and illustrated on the right. The structures in (c) and (d) are rotated about the dimer interface relative to those in (a) and (b) as indicated by the rotation arrows. |
![[Figure 2]](ic5119fig2.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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