Structural Refinement of V-ATPase

Maps from DeepEMhancer were used for model building, refinement, and subsequent structural interpretation. The V₁EG model of the V/A-ATPase was adopted from the 3.1 Å V₁EG structure (PDB accession no. 7VAL) as the initial model (23 (link)). With 2.5 to 3.1 Å V₁EG density maps, we could model side chains and local geometry to achieve higher accuracy (Fig. S7A). The initial model was docked into the cryo-EM map using UCSF ChimeraX (42 (link)), and sulfate ions were built into COOT (43 (link)), followed by several rounds of real-space refinement using Phenix (44 (link), 45 (link)). The initial model manually corrected residue by residue in COOT (43 (link)) regarding side-chain conformations. The iterative process using COOT (43 (link)) and ISOLDE (46 (link)) was performed for several rounds to correct the remaining errors until the model agreed well with the geometry (Table S2). Cross-validation was carried out by comprehensive validation in Phenix (44 (link), 45 (link)), and the map to model Fourier shell correlation curves was calculated (Fig. S7B). Root means square displacement values between the atomic models and structural figures were calculated using the UCSF chimeraX (42 (link)).