The plasma membrane potential and secondary transport systems in all eukaryotes are energized by the activity of P-type ATPase membrane proteins: H+ATPase (the proton pump) in plants and fungi and Na+, K+- ATPase (the sodium-potassium pump) in animals. The overall shape of proton pumps has been revealed by electron microscopy. The crystal structure of AHA2, a plasma membrane H+-ATPase isoform of Arabidopsis thaliana, by X-ray crystallography at 3.6 Å was available. The isoform is expressed mainly in root. In the present study homology modeling along with transmembrane topology predictions has been used to build the atomic model of AHA1, another plasma membrane H+-ATPase isoform of Arabidopsis thaliana expressing in both root and shoot. AHA2 was used as the template. The homology modeling was done using the MODELLER9v2 software. The model energy was minimized by applying molecular mechanics method. The root mean square deviation (RMSD) for C atoms between the X-ray and the homology-modeled structures was 0.4 Å. Ten transmembrane helices (TM1- TM10) in the model were identified. The final model obtained by molecular mechanics and dynamics method was assessed by PROCHECK and VERIFY 3D graph, which showed that the final refined model is reliable. Asp684 of AHA1 is suggested to act as an essential proton acceptor during proton translocation. The residue may also participate in defining the E1 proton-binding site. Despite difference in the tissue-specific expression of the two proteins, no remarkable difference in their structure was observed, suggesting that the enzyme isoform evolution may not be linked to its tissue-specific expression.