Vesicular monoamine transporter 2 (VMAT2) catalyzes transport of monoamines into storage vesicles in a process that involves exchange of the charged monoamine with two protons. VMAT2 is a member of the DHA12 family of multidrug transporters that belongs to the major facilitator superfamily (MFS) of secondary transporters. Here we present a homology model of VMAT2, which has the standard MFS fold, that is, with two domains of six transmembrane helices each which are related by twofold pseudosymmetry and whose axis runs normal to the membrane and between the two halves. Demonstration of the essential role of a membraneembedded glutamate and confirmation of the existence of a hydrogen bond probably involved in proton transport provide experimental evidence that validates some of the predictions inherent to the model. Moreover, we show the essential role of residues at two anchor points between the two bundles. These residues appear to function as molecular hinge points about which the two six transmembrane-helix bundles flex and straighten to open and close the pathways on either side of the membrane as required for transport. Polar residues that create a hydrogen bond cluster form one of the anchor points of VMAT2. The other results from hydrophobic interactions. Residues at the anchor points are strongly conserved in other MFS transporters in one way or another, suggesting that interactions at these locations will be critical in most, if not all, MFS transporters.ion coupling | multidrug resistance | membrane proteins | neurotransmitter transporter | homology modeling T ransport and storage of neurotransmitters in synaptic vesicles allow their regulated release from the presynaptic cell into the synaptic cleft. The neurotransmitter molecules are accumulated in synaptic vesicles by vesicular neurotransmitter transporters (1-3). Transport of monoamines (serotonin, dopamine, histamine, adrenaline, and noradrenaline) is carried out by the vesicular monoamine transporter (VMAT) family, which includes two isoforms, VMAT1 and VMAT2, in a process that involves the exchange of two protons for one substrate molecule (1-3). The proton electrochemical gradient necessary for transport is generated by the vesicular H + -ATPase (V-ATPase). The structural basis for the function of VMAT remains unknown. VMAT2 is a member of the DHA12 family of multidrug transporters that belongs to the major facilitator superfamily (MFS) of secondary transporters. Most MFS transporters contain 12 transmembrane (TM) helices, and crystal structures revealed that the 12 TM helices are arranged in two domains of six TMs each, which are related by a twofold pseudosymmetry with an axis that runs normal to the membrane and between the two halves (4-9). Furthermore, analysis of the lactose permease (LacY) crystal structure revealed the presence of inverted topology repeat units within each of the domains (10). That is, the first three helices of each domain are structurally related to the second three helices of that domain by a twofold pseudosymmetry ax...