Table 1. Available structural models of VMATs
NamePMDB codeTemplateIdentityConformationProQM scoreReference
%
CcytN/ALacY 1PV6∼12aCytoplasm facing0.561Vardy et al., 2004
CcytPM0078823LacY 1PV7∼12Cytoplasm facing0.616Yaffe et al., 2013
ClumPM0078824LacY 1PV7-RSM∼12Lumen facing0.616Yaffe et al., 2013
ClumPM0080553YajR 3WDO∼18Lumen facing0.717Yaffe et al., 2016

Structural models of rat VMAT2 have been reported in two alternate conformations. Three of these are available from the Protein Model Database (PMDB; Castrignanò et al., 2006). The models were built using different x-ray structure templates and, in one case (Clum), a repeat-swapped model as a template; the underlying sequence alignments also differ. Identity: the percentage of identical residues in the target and template sequences in the region of the target that was modeled. The structural quality of the models is estimated by the ProQM score, which takes values of 0 to 1, and where higher values indicate better consistency with known structures (Ray et al., 2010). For reference, the ProQM scores of the templates are 0.729 (Protein Data Bank accession no. 1PV7) and 0.741 (Protein Data Bank accession no. 3WDO). N/A, not applicable.

  • a For the Ccyt model, the sequence identity was estimated from a TMalign structural alignment of the model to its template.