Table 1. Available structural models of... | Rockefeller University Press

Table 1.

Available structural models of VMATs

Name	PMDB code	Template	Identity	Conformation	ProQM score	Reference
			%
C_cyt	N/A	LacY 1PV6	∼12^{^a}	Cytoplasm facing	0.561	Vardy et al., 2004
C_cyt’	PM0078823	LacY 1PV7	∼12	Cytoplasm facing	0.616	Yaffe et al., 2013
C_lum	PM0078824	LacY 1PV7-RSM	∼12	Lumen facing	0.616	Yaffe et al., 2013
C_lum’	PM0080553	YajR 3WDO	∼18	Lumen facing	0.717	Yaffe et al., 2016

Name	PMDB code	Template	Identity	Conformation	ProQM score	Reference
			%
C_cyt	N/A	LacY 1PV6	∼12^{^a}	Cytoplasm facing	0.561	Vardy et al., 2004
C_cyt’	PM0078823	LacY 1PV7	∼12	Cytoplasm facing	0.616	Yaffe et al., 2013
C_lum	PM0078824	LacY 1PV7-RSM	∼12	Lumen facing	0.616	Yaffe et al., 2013
C_lum’	PM0080553	YajR 3WDO	∼18	Lumen facing	0.717	Yaffe 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 (C_lum), 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.

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

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