Extended Data Fig. 7: Interbundle salt bridges, botulinum neurotoxin E-luminal domain interaction analysis, and SLC22 family intracellular domain comparison.
From: Structures of synaptic vesicle protein 2A and 2B bound to anticonvulsants
a. Alignment of the SV2A luminal domain with the crystal structure of the chimeric SV2A-SV2C luminal domain complexed with botulinum toxin serotype E (BoNTE, electrostatic surface), specific to SV2A and SV2B (PDB 7UIB). Y535 and Y557 are essential for BoNTE binding. Residues in the SV2A luminal domain provide charge complementarity to the BoNTE surface. b. The SV2B luminal domain aligned with 7UIB, residues in the SV2B luminal domain provide charge complementarity to BoNTE. Y478 and Y500 are important for BoNTE binding. c. The SV2C luminal domain (PDB 5JMC) aligned to 7UIB. Residues analogous to SV2A Y535/SV2B Y478 and SV2A Y557/SV2B Y500 are T521 and E543 in SV2C, which disrupt binding to BoNTE. d. Comparison with luminal domain structures (green: 5JMC; light blue: 7UIA; hot pink: 6ES1) with the cryo-EM structure of SV2B (light pink). e. A salt bridge between E194 and R473 in SV2A is observed above the closed luminal gate (spheres). D471 is conserved amongst all 3 SV2s. Sidechain density is shown in light blue. f. A salt bridge between K146 and D413 in SV2B is observed above the closed luminal gate (spheres), with water-like density near the two sidechains. Sidechain and water density is shown in light blue. g. Alignment of the SV2A (green) and SV2B (light blue) intracellular domains with the intracellular domains of human organic cation transporter 1 (pink, PDB 8ET7) and rat organic anion transporter 1 (tan, PDB 8BW7). h. A salt bridge between E282 and R682 in SV2A is observed below the closed intracellular gate. Sidechain density is shown in light blue. i. A salt bridge between E225 and R623 in SV2B is observed beneath the closed intracellular gating residues (spheres). Sidechain density is shown in light blue. j. In the UCB-2500 (pink sticks) binding site, a salt bridge is formed between D179 and K694, between the closed luminal and intracellular gates (spheres). Sidechain density is shown in light blue. k. In the PSL binding site, a salt bridge is formed by D122 and K635 in between the closed luminal and intracellular gates (spheres), with water-like density. Sidechain and water density is shown in light blue.
