Table 1.

Comparison of amino acid sequences for human and rat NMDA receptor subunits.

	Signal peptide # of residues		ATD # of residues		ABD # of residues		TMD # of residues		CTD # of residues		Total subunit # of residues
	non- identical	total	non- identical	total	non- identical	total	non- identical	total	non- identical	total	non- identical	total
GluN1	3	20	3	376	1	286	0	106	0	150	7	938
GluN2A	4	27	14	377	2	275	0	158	49	627	69	1464
GluN2B	2	28	1	376	2	276	0	158	18	646	23	1484
GluN2C	14	19	28	395	6	276	3	158	111	388	162	1236
GluN2D	0	25	15	402	0	277	0	158	44	474	59	1336

NMDA receptor subunits consist of the extracellular amino-terminal domain (ATD), the agonist binding domain (ABD), the transmembrane domain (TMD), and the intracellular carboxyl-terminal domain (CTD). Insertion or deletions in human subunits compared to rat subunits are also categorized as non-identical positions. ATD includes the ATD-S1 linker, and TMD is M1M2M3 including pre-M1 and intracellular loops. The ABD is S1 and S2 as well as S1-M1, M3-S2, and S2-M4 linkers. The amino acid sequences of all rat ionotropic glutamate receptor subunits were aligned using the ClustalW algorithm and the regions for each of the NMDA receptor subunits were determined based on GluA2 in this global alignment. In GluA2, the regions were defined as amino acids 1–397 (signal peptide and ATD), 398–414 (ATD-S1 linker), 415–527 (S1), 528–534 (S1-M1 linker), 535–647 (M1M2M3), 648–652 (M3-S2 linker), 653–794 (S2), 795–809 (S2-M4 linker), 810–833 (M4) and 834–884 (CTD). Signal peptides were predicted using the SignalP 3.0 server (Bendtsen et al., 2004). The GenBank IDs for amino acid sequences of human subunits used in the alignment are listed in Materials and Methods. NP_015566.1, NP_000824.1, NP_000825.2, NP_000826.1 (and NP_000826.2), and NP_000827.1 were used in the alignment for rat GluN1, GluN2A, GluN2B, GluN2C, and GluN2D, respectively.