Extended Data Fig. 2: Structural details of the GBP1-GDP·AlF₃ dimer.

(a) Comparison of GBP1-GDP·AlF₃-Nb74 reconstructions without (C1) or (b) with C2 symmetry imposed. Imposing strict C2 symmetry results in artefacts at the C-terminal end of the MD. (c) Location of the GDP·AlF₃ ligand at the dimer interface and close-up of the catalytic site with the ligand in stick representation superposed onto the cryo-EM density. The catalytic arginine R48 and residues proximal to the ligand are highlighted. (d) GDP·AlF₃ with corresponding density. (e) Charged residues at the interface between the MD are displayed for one of the monomers. The electrostatic potential is mapped to the surface representation of the other monomer. The resolution of the EM density map in this region precluded unambiguous modelling of side chains. Preferential rotamers are shown without reference to potential interactions. (f) and (g) Close-up of the MD interface. Residues with opposing charges locate to either side of the interface, potentially stabilising the parallel arrangement of the MDs. (h) Atomic coordinate models of the GBP1 (left) and GBP5 dimer (right; residues 1–487, PDB: 7E5A). (i) Overlay of both atomic models. (j) Comparison of monomer subunits. The main differences are in the orientation of the MD relative to the LG domain, with the MD in the GBP1 dimer displaying a larger twist relative to the long axis (RMSD over all Cα atoms: 4.46 Å). (k) Separate alignment of LG domain (residues 1–306) and MD (residues 317–483) allows improvement of the fit, suggesting the main determinant of the differential twists is the cross-over linker. (l) Close-up of the dimer interfaces at the base of the MD. Likely interacting residues from PISA analysis are shown. Map quality in this area precludes modelling of side chain conformations. (m) Close-up of superposed cross-over linkers for GBP1 (dark blue) and GBP5 (grey). (n) Close-up of the hydrophobic plug of GBP1 (dark blue and light green) and GBP5 (grey). Putative residues stabilising the cross-over arrangement are highlighted. (o) Locally sharpened density maps (LocScale2³⁹) reveal additional density protruding from helix α11 consistent with a flexible GED. (p) The LocScale map also allowed tracing the α3-α3′ loop (residues 156 to 167; light blue).