Figure 7. Localization of ArfGAP2 within the COPI coat.
(A) COPI-ArfGAP2 leaf structure as grey isosurface. (B) COPI leaf structure (grey) and the difference map between the COPI and the COPI-ArfGAP2 structure (red). (C) The fit of COPI and the ArfGAP2 catalytic domain (PDB:2P57) into the COPI-ArfGAP2 leaf structure. The domain is located near the Arf1-nucleotide binding site (nucleotide is shown in green) (D) Surface representations of the COPI and ArfGAP2 molecular models, illustrating the position of the ArfGAP2 catalytic domain (red) in a niche within the assembled coat. See also Figure 7—figure supplement 1.
Figure 7—figure supplement 1. Position of the ArfGAP2 catalytic domain within in the COPI coat.
(A) The COPI-ArfGAP2 dataset was split into two distinct classes by multireference-based alignment and classification. Slice through the EM density of the class 1 from the COPI-ArfGAP2 dataset, which contains the extra density corresponding to the ArfGAP2 catalytic domain. The slicing plane is orthogonal to the membrane. The additional density is marked with an arrow. (B) Slice through the EM density of the class 2 from the COPI-ArfGAP2 dataset, which did not contain any additional densities in comparison with the control structure. The slicing plane is orthogonal to the membrane. (C) Position of the catalytic domain (red) and ankyrin domain (cyan) based on the Arf6-ASAP3 structure (PDB:3LVQ). The Arf1 from the Arf6-ASAP3 structure was superimposed with the Arf1 in our model. Note, that the ankyrin domain clashes with the β-COP (dark green). The existence of a small COPI-niche suggests that there may be sterical selection for the type of ArfGAP protein interacting with Arf1 in the context of the COPI coat. (D) Position of the catalytic domain (red) based on the Arf1-ArfGAP1 structure, where Arf1 in the Arf1-ArfGAP structure was superimposed on the Arf1 in our model (Goldberg, 1998). Note, that the catalytic domain is far from the nucleotide site (nucleotide is shown in green). Color scheme: Arf1 - pink, γ-COP – light green, β-COP - dark green, ζ-COP - yellow, δ-COP - orange, β’-COP - light blue, α-COP – dark blue. Compare panels C and D with our structural model illustrated in Figure 7C).