A high-affinity homomeric, non-NMDA glutamate receptor was previously purified from the amphibian Xenopus laevis. We have obtained nine peptide sequences from its subunit, applied in cDNA cloning. The cDNA encodes a subunit (XenU1) containing all nine sequences. The 51,600-dalton mature subunit has four hydrophobic domains homologous to the four in the C-terminal half of mammalian non-NMDA receptor subunits. Transient expression in COS cells showed 1:1 binding (at Bmax) of [3H] kainate (KD = 9.1 nM) and of [3H] AMPA (alpha-amino-3-hydroxy-5-methyl-isoxazole-4-propionic acid; KD = 62 nM). The competitive binding series domoate > kainate > AMPA > NBQX > glutamate was established (where NBQX is 2,3-dihydroxy-6-nitro-7-sulphamoyl-benzo (f) quinoxaline). Each agonist shows the same KI value against [3H] kainate and [3H] AMPA binding, suggesting a common agonist site, but two conformations thereof are distinguishable by their different affinities for the antagonist NBQX and by the allosteric effect of thiocyanate anion (greatly potentiating AMPA binding, inert with kainate). XenU1 is exceptional among non-NMDA receptor subunits because it lacks most of the large N-terminal domain found in those of mammals and it has high affinity for both kainate and AMPA. It differs from the similarly-short "kainate-binding proteins" (KBPs), in binding AMPA and in forming glutamate receptor channels when the native protein is reconstituted. Moreover, whereas a full-length kainate receptor of mammals, GluR6, is shown here (from a partial cDNA sequence) to exist also in Xenopus, with approximately 97% sequence identity to rat GluR6, XenU1 is much less homologous to any rat kainate or AMPA receptor and also to the KBPs, even from another amphibian, Rana. Another difference is that a potential concensus sequence ("EF hand") for Ca2+ binding is present in the N-terminal domain of XenU1, but not in the chicken (glial) KBP. XenU1 is deduced to be in a new family of non-NMDA receptors.